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BioImaging Systems User manual

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1. Note You can also display the Browser by pressing Browse in the Open dialog box see page 8 2 ll Browser Desktop demo62x sqd demo62 sqd a g My Computer H E 3 Floppy 4 Eg Win 98 C ii 2 My Documents i Y Newfonts p j a Program Files H E Accessories C GeneDirectory ESTE ETS 4 03 GeneSnap 2 3 GeneTools C Backup CI Demo Chemi Images C Demo Colony Images 3 Demo Gel Images C Demo Spotblot Images CI Getting Started democt democtsad democ democ4sga C Images 07 GrabberSupport Intemet Explorer Q Microsoft Hardware 4 Microsoft Office Microsoft Script Control The Browser is displayed in the GeneSnap Application window document area with any open Image windows when you first display it it will be maximized and will cover any open Image windows The Browser can be maximized minimized restored and moved in the same way as Image windows It is also tiled cascaded and arranged with the Image windows using commands in the Window menu However unlike Image windows there is no tab for the Browser at the bottom of the GeneSnap Application window document area you can select it by choosing it from the list of open windows at the bottom of the Window menu or by clicking in it To open an existing image file using the Browser 1 Use the left hand pane in the Browser in exactly the same way as you use the
2. To sharpen the image make the boundaries between areas sharper in the active Image window Choose Sharpen from the Image menu Biolmaging Systems User Manual 5 23 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap The effect of sharpening an image is to increase the fine detail in the image the high spatial frequencies by adding the difference between the original image and a locally averaged version To smooth the image make the boundaries between areas less sharp in the selected image window Choose Smooth from the Image menu JS The smooth operation is carried out by calculating a local average for each pixel in the image When you sharpen or smooth an image there is a loss of image information Applying speckle correction MultiGenius only Defective elements in CCD cameras can cause isolated bright pixels to appear in images Speckle correction can remove these by comparing each pixel value with the average of the neighboring eight pixels If the value is greater than the average by more than a threshold amount it will be replaced by the average value To apply speckle star field correction to an image Press the speckle correction button in the Image toolbar When you speckle correct an image there may be a loss of image information Inverting images To invert an image swap black and white for a grey scale image or
3. 2 12 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Analyzing the image Analyzing the image The next step after capturing the image is to analyze it to do this you will use SYNGENE s GeneTools To start up GeneTools to analyze the image in the selected Image window it Fa 1 Press the Send to GeneTools button A standard Windows Save As dialog box will open so that you can save the image file Save in Y Images es exi Image1 sgd Image2 sgd W Image3 sad pl Image4 sgd M Image5 sad Image6 sgd File name Image sad L 3 j Save as type GeneSnap sgd Cancel A 2 Select a folder to hold the image file from the Save in drop down list and the file list box below it 3 Enter a name for the image file in the File name box 4 Press Save to save the image with the new name Once you have saved the image GeneTools will open with the image loaded ready for you to analyze it see your GeneTools documentation for how to use GeneTools Biolmaging Systems User Manual 2 13 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneGenius MultiGenius or ChemiGenius Hints This section gives a few further hints for how to work with GeneGenius or MultiGenius to capture the best quality images Starting G
4. e 1 18 Software overview w st moida a aa d aao eue aua ae noie i ae Ta i ao e 1 19 GeneSmapy ari 105 a oe widen OS E a e a a oa A a a 1 19 G neTOolss sua a ae ae a a a a ee Oe o a S 1 20 SUMMA i a m do p aE ee e E ee Oe ake God GU 2 1 20 Getting Started with GeneGenius MultiGenius or ChemiGenius 2 SWIMMING OM 2 s BAC eae ee Bw A So MAD Ae e a 2 1 Capturing an Image s 4 c e wos wae Se e ee ee a e A 2 3 Framing and focusing the image des woe we dw ew 2 3 Capturing an image using automatic exposure 2 2 1 ee ee 2 5 Biolmaging Systems User Manual Contents 1 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Contents Capturing an image from live video 2 s s e coso ee 2 6 Capturing a series of images p o i sog oaa oa i d oa e a a A 2 8 Capturing an image with Extended Dynamic Range 2 12 Analyzing the image os s ow seden aa wiae a a ea 2 13 HINS c ob oe oO AB SE EEL ABS REE e a e e ESE e e EEE SS 2 14 Starting GeneSmap s e a e ec ee Se A a Bw ie 2 14 LOGGING IN 3 to eo eR we OLE de See wd ele oe wea Se ee 2 14 Displaying the Image Capture toolbox 2 a a a 2 14 Image EXPOSUTE au kw ae a GE he ee eG a e G 2 15 FOCUSING p x a a e Oui i ee Gt te ed ek a le ae ea Se 2 16 Saturation detection s asotir se eee ea ee eB te ee eB 2 16 MOVING ON s ox pis a RA Soe Pe a AOR a Rd Re a 2 17 Getting Started w
5. Note Each camera is factory configured to give optimum results with the specific lens fitted to it It is vital that you do not make any adjustments to this configuration in particular you must not detach the lens from the camera before fitting To fit the camera lens assembly in the Darkroom 1 Remove any packaging from the top of the Darkroom Note the two mounting brackets with slotted holes which will be used to mount the camera lens assembly Also note the circular hole in the side of the light tight cover with its rubber sealing pad the lens barrel will be fitted in this hole 2 Pass the lens barrel into the hole in the side of the Darkroom and fix the camera lens assembly to the two mounting brackets using the allen bolts provided one bracket attaches to the camera the other to the lens Biolmaging Systems User Manual 1 7 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Introduction and Initial Setup Note Make sure that the lens is pressed firmly against the black sealing pad in the light tight wall before finally tightening the allen bolts do not tighten the lens bolt more than finger tight 3 If the braided camera cable has already been fitted between the back of the camera and the Darkroom go straight to Step 6 Otherwise take the braided camera cable and fit the D connector to the matching connector in the Darkroom it is
6. 5 44 The GeneSnap Application Window 6 Status Bats z s A oe aoe GAS Ee A EE Aes BEA DS BE Ree 6 2 Image Capture toolbox s gaa BaP Re aa Rw 6 2 Docking and floating the Image Capture toolbox 2 2 2 2 6 4 Door drawer icons a a x ace mir aia ae e e a e a A a ae a a ASE a a 6 5 Freeze Go live not GeneGnome a a a a a a a a a a a a 6 5 Single exposure GeneGnome only 2 a a 6 6 Open drawer GeneGnome and GeneWizard only 6 6 Iris controls not GeneGnome or GeneWizard 2 2 220282 6 7 Zoom controls not GeneGnome or GeneWizard 2 202282 6 7 Focus controls not GeneGnome or GeneWizard 2 2 2 2202282 6 7 EXPOSUETIMGS le aga Re ae oh ek et E ed ae Ee d 6 8 Automatic exposure not GeneGnome 2 2 ee ee 6 8 IMAGE SHES os lt aw ee Be a a ee a A A RA 6 9 Lighting control not GeneGnome 2 2 e e 6 9 Extended Dynamic Range EDR control not GeneGnome 6 11 Sensitivity resolution ChemiGenius2 only o o ee 6 11 Filter wheel control not GeneGnome or GeneWizard 2 202 2 6 12 Image WICIOWS 2 ac o eS bee ee EG Aa aaa 6 12 Zooming and scrolling Image windows 2 ee 6 13 Image Controls 5 4 iG ae el a SG eG Ge ea ai 6 16 Original and Processed View modes 2 a a e eo o 6 17 The Histogram windows o s a aa eaa Beda edad waea Bee 8 6 18 Showing and hiding the Histogram window oo ooa a a
7. To select which lighting to use in the Darkroom Select the required option from the Lighting drop down list box For GeneGenius MultiGenius and ChemiGenius you can select No light Transilluminator Epi long wave UV standard for ChemiGenius otherwise available as an option Epi short wave UV standard for ChemiGenius otherwise available as an option Upper white Lower white For GeneWizard you can select No light Transilluminator The operation of the lighting is completely automatic For example the selected lighting is turned on automatically when you create a new Image window showing a live image or when you press the Freeze Go live button to display a live image The lighting is then Biolmaging Systems User Manual 6 9 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The GeneSnap Application Window turned off automatically when you freeze the image Similarly the lighting is turned on if necessary and off automatically when you perform an automatic exposure or image series capture Note As a safety measure the UV lighting will only turn on if the Darkroom door is closed unless you have deliberately disabled the door safety interlock see page 5 11 to work with an open door If a live image is displayed with UV lighting selected the lighting will turn off automatically if you open the door and switch on again when the door is closed
8. will be displayed in an Image window a new Image window will be opened if required However if the first capture produces an image with saturated areas GeneSnap will carry out another capture but with a shorter exposure time repeating this procedure if necessary until the captured image contains no saturated areas GeneSnap then uses this exposure time as the basis for taking three more exposures with doubling exposure times Note If GeneSnap is unable to capture an image without saturating even at its shortest exposure time it will display a dialog box saying that it is unable to carry out the EDR capture and suggesting that you close down the iris to reduce the aperture Note If EDR is set for a series exposure see page 5 7 this procedure will be repeated for each image in the series Because of the long exposure times required you are recommended not to use a series capture with EDR for chemiluminescence applications Using the UV light with the Darkroom s door open Note This section does not apply to GeneGnome or GeneWizard For safety reasons if the Darkroom s door is open the UV lights are not turned on when you display a live image or capture an image Similarly the UV lights are turned off if you open the Darkroom door while you are displaying a live image or capturing an image However there are occasions when you may want to work on a gel illuminated by UV light from the transilluminator
9. Choose Contents from the Help menu To display specific help for a command or area of the GeneSnap Application window ho 1 Press the context sensitive help button in the Standard Toolbar choose Standard Toolbar in the View menu to display the Standard Toolbar if it is hidden The pointer will change to the Help pointer R 2 Select the command or click on an area of the window to display help for that item Index To display the Index tab for the Help System Choose Index from the Help menu Using Help To display help for using the Help System Choose Using Help from the Help menu 8 38 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Help Show Wizard To display a Wizard to give you a quick tour of the program Choose Show Wizard from the Help menu Change Wizard To change the animation character used for the Wizard 1 Choose Change Wizard from the Help menu to display the Character Properties dialog box 2 Press the Next and Back buttons to preview the different characters 3 When the required character is displayed press OK to select the character and close the dialog box About GeneSnap To display the About GeneSnap dialog box to view information about the version of GeneSnap you are using Choose About GeneSnap from the Help menu The About GeneSnap dialog box shows the registered serial number of the copy of the
10. Choose Crop to Region from the Image menu Note If you print a cropped image using a Sony UPD895 thermal printer the cropped area will be magnified to fill the page When you crop an image there is a loss of image information Reshaping the region of interest To reshape the region of interest 1 Click in the region of interest to select it drag handles will appear at its corners and the middle of each side Reshape the rectangle by dragging the relevant handle the pointer changes shape when it is over a handle showing that you can drag it Moving the region of interest To move the region of interest 1 Move the pointer into the region of interest 5 26 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Placing annotations on an image 2 Press the mouse button and drag the region of interest to its new position When you press the mouse button the region of interest becomes selected drag handles appear at its corners and the pointer changes to a four headed arrow showing that you can drag the region to a new position Deleting the region of interest To delete the region of interest 1 Click in the region of interest to select it drag handles will appear at its corners and the middle of each side 2 Press Placing annotations on an image Note The procedures in this section describe ho
11. aN 1 Press the Draw Arrow button Biolmaging Systems User Manual 5 39 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap 2 Move the pointer to the position where you want to place the tail of the arrow When the arrow drawing tool is selected the pointer changes to a cross hair when it is over the image w Nw a a Ns a i it ld tg ra v ee ee X 3 Press and hold down the mouse button then drag to the position where you want to place the head of the arrow et w Va o a ae hi et T aa or ee ee 4 Release to place the arrow head on the image w du A ed Ns T ae gS _ When you have placed the arrow on the image the Draw Arrow tool will still be selected so that you can place other arrows on the image If you select the arrow annotation using the Select tool drag handles appear on the head and tail of the arrow so that you can move or reshape the arrow 5 40 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Placing annotations on an image Note You can select the Select tool when the Draw Arrow tool is selected by pressing the Select button on the Annotate toolbar Changing annotations Selecting annotations To select an individual annotation R 1 If it is not already selected select the Selector to
12. A rtisan Artisan Technology Group is your source for quality Technology Group new and certified used pre owned equipment FAST SHIPPING AND SERVICE CENTER REPAIRS WE BUY USED EQUIPMENT DELIVERY Experienced engineers and technicians on staff Sell your excess underutilized and idle used equipment TENS OF THOUSANDS OF at our full service in house repair center We also offer credit for buy backs and trade ins IN STOCK ITEMS www artisantg com WeBuyEquipment 7 EQUIPMENT DEMOS HUNDREDS OF InstraV ea REMOTE INSPECTION LOOKING FOR MORE INFORMATION MANUFACTURERS Remotely inspect equipment before purchasing with Visit us on the web at www artisantg com 7 for more our interactive website at www instraview com information on price quotations drivers technical LEASING MONTHLY specifications manuals and documentation RENTALS ITAR CERTIFIED CEP BAD tia Contact us 888 88 SOURCE sales artisantg com www artisantg com Biolmaging Systems User manual All possible care has been taken in the preparation of this publication but Synoptics Limited accepts no liability for any inaccuracies that may be found Synoptics Limited reserves the right to make changes without notice both to this publication and to the product that it describes No part of this publication may be reproduced stored in a retrieval system or transmitted in any form or by any means electronic mechanical photocopying recording or otherwise
13. Guaranteed 888 88 SOURCE www artisantg com The GeneSnap Application Window Status Bar You can choose to display or hide the Status Bar at the bottom of the GeneSnap Application window by choosing Status Bar from the View menu The left hand end of the Status Bar shows the text LIVE when a live image is being displayed Other information is shown in a number of boxes in the Status Bar Other information is shown in a number of boxes in the Status Bar From left to right they display e The leftmost box is always blank e In brackets the X and Y position of the pointer over a captured image followed by the intensity of the image pixel at the pointer the box does not show any information for a live image e For GeneGenius MultiGenius ChemiGenius or GeneWizard with the Histogram window hidden e The Brightness Contrast and Gamma settings For GeneGenius MultiGenius ChemiGenius or GeneWizard with the Histogram window displayed and for GeneGnome whether the Histogram window is displayed or hidden e The image intensity represented by Black in the image display this is the position of the left hand cursor if the Histogram window is displayed the image intensity represented by White in the image display this is the position of the right hand cursor if the Histogram window is displayed and the Gamma setting e The size in pixels and grayscale depth in number of bits of the image e The magnification of the
14. Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Appendix PC Board and Software Installation 7 Press Next to display the Install Wizard Electronic Mail dialog box 8 Select Create a message for me if you want the Install Wizard to compile and send an email message to SYNGENE requesting the security key otherwise select Tell me what to send Note YOU MUST SEND ALL THE INFORMATION GIVEN 9 Press next to compile and send the email message or display the Install Wizard Code Request dialog box You can press a button to print the request so that you can fax it to SYNGENE or save the text of the request in a text file Note The email key issuing system at SYNGENE uses an automatic response program Your message should only include the installation request since any other text will be ignored The message body of the installation request should consist of the six lines from the Install Wizard any changes you make to the format of the message may prevent the automatic system from issuing your security code Note The Installation Wizard determines the Request Key you send to SYNGENE on the basis of the media key and the current configuration of the PC The Security Code is then based on the Request Key This means that you should not change the configuration of the PC by installing or removing hardware for example between sending the Request Key and entering the Security Code It a
15. 0 so bem kd we ke oe he he ee Bbw he we OD he he ae 8 35 EMBOSS sce e g Ban Ro GAR RR BA oe SO aA ee we 8 35 Define Region of Interest 2 2 e eo 8 36 Crop to REGION cos ww en waa a Gere a ee a GS 8 37 Help s w opa eG EE ae Re Ea ee A we we ee a 8 38 Contents e RA aie Be Gs ee ete hate ae Gece A Bee a 8 38 INDEX 8 rad Ss we a Bd phe Gate ead E ee a 8 38 Using Helpis a ea ie pad een ee a Gab dea AA 8 38 Biolmaging Systems User Manual Contents 7 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Contents SMOWIWIZATO skies a ang eek hes ao hota te hae ae He a a a 8 39 Change Wizard 6 st a4 fee bed ae ba rks fk a ee eS 8 39 About GeneSnap sse ses anaya at t adi d ea e a io 8 39 Appendix PC Board and Software Installation A Installing GENETOOS ss a ah ee ma ee a eee od do Bas ds A 1 Installing BONOS pos ane Gogoa a a aa ak ak Reco a E a A 3 Installing GRES a ys i a ah ook e he ew Re wk ee A we Bw S A 4 Checking the driver installation in Windows 95 98 XP Pro A 5 Disabling drivers in Windows NT 2 2 2 A 5 Contents 8 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Part Introduction and Initial Setup Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Artisan Technology Group Quality Ins
16. Al cl 28 Image6 sad File name Image sgd es j Save as type GeneSnap sad y ancel 2 Select a folder to hold the image from the Save in drop down list and the file list box below it 3 Enter a name for the image file in the File name box 4 Press Save to save the image with the new name If you have processed the image in any way both the Processed and Original images will be saved together with any annotations you have placed on them If you reopen the image in GeneSnap you will be able to use View Original or View Processed to Biolmaging Systems User Manual 8 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Menus view both versions and the annotations will still exist as separate objects that can still be moved or edited as required Close Image To close the selected Image window Choose Close Image from the File menu If the Image window contains an unsaved image grabbed from the camera or if you have made any changes to it since it was last saved you will be asked if you want to save the changes Export Image Note You use Save Image As to save the image in GeneSnap sgd format for Good Laboratory Practice purposes you can reopen images saved in this format in GeneSnap using Open Image You use Export Image to save images in a wide range of other image formats you will be able to open these images in paint progr
17. GeneSnap will also turn the lights off automatically if a live image is left displayed for more than ten minutes a dialog box will be displayed warning you and giving you the option to turn the lights back on When the lighting is turned on to show a live image or during an automatic exposure or image series capture the lighting graphic in the Image capture toolbox is lit up appropriately for example A Epi long wave uv Transilluminator M E Lowerwhte _ Upper white gt Note The red lamp on the front of the Darkroom shows when the camera is displaying or capturing for example during automatic exposure or image series capture a live image the Lighting control graphic shows the state of the illumination Although these are often linked they are not the same for example if you open the door when showing a live image with UV lighting the red lamp will stay lit but the graphic will show that the UV light has been turned off automatically When Transilluminator is selected you can double click on the lighting graphic to override the door safety interlock to work with a live image with the UV light on and the door open see page 5 11 for details 6 10 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Image Capture toolbox Extended Dynamic Range EDR control not GeneGnome To use a
18. Note In accordance with Good Laboratory Practice you can only load sgd secure image files The sgd secure image files can also be opened in GeneTools which also accepts tiff bmp and JPEG files To load a previously saved image file LS 1 Choose Open Image from the File menu to display a standard Windows Open dialog box Open BEI Lool ME Image6 sad Files of type SynGene Data sgd y Cancel Browse 2 Select the folder holding the image file using the Look in drop down list and the file list box below it 3 Select the required file by clicking on it in the file list box 4 Press Open to open the image file in a new Image window 5 18 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Saving and loading image files If the image had been processed in any way see the following section before it was saved both the Processed and Original images will be opened choose View Original or View Processed from the View menu to choose which version to view If there were any annotations on the image when it was saved the annotations will still exist on the image as separate objects that can be moved or edited as required Note You can also load images using the Browser see page 6 22 for details Creating a composite image multiplexing Sometimes different parts of a gel require different type
19. arrow at the left hand end of the control to increase or decrease the number 00m Ejs 000ms Note You can also increase or decrease the exposure time by pressing the up or down arrow keys on the keyboard or if you are using a wheel mouse by turning the wheel c If required select another section hours minutes seconds or milliseconds and edit that number you can click on the scroll bars at the right hand end of the control to move the selection to the next section E 00m 04s Mims IN Note Only certain values of exposure time are allowed if you type a non allowed value directly into the box it will be corrected to the next allowed value The values allowed depend on the system you are using There are a number of issues affecting the best combination of exposure time and iris setting e While you are adjusting the gel position and setting the zoom and focus you should use a short exposure time and wide iris setting This means that the image will respond quickly to any changes you make It also means that you will be able to set Biolmaging Systems User Manual 2 15 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneGenius MultiGenius or ChemiGenius a more accurate focus as the depth of field will be less but see the next point for when you actually capture the image e If you have a thick gel you will get better f
20. as above or filled on the toolbar depending on whether hollow or filled shapes is selected Select Pe Press the Select button to select the Selector tool so that you can select an annotation or Region of Interest see page 8 36 by clicking on it You can also select the Selector tool by clicking in an Image window if one of the annotation tools is selected and you are not part way through drawing the annotation There is no menu command equivalent to pressing this button Draw Line N Press the Draw Line button to draw a line annotation on an image see page 5 28 for details There is no menu command equivalent to pressing this button Draw Rectangle Press the Draw Rectangle button to draw a hollow or filled rectangle annotation on an image see page 5 30 for details There is no menu command equivalent to pressing this button 7 4 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Annotate Draw Ellipse Press the Draw Ellipse button to draw a hollow or filled ellipse annotation on an image see page 5 31 for details There is no menu command equivalent to pressing this button Draw Freehand Shape lt Press the Draw Freehand Shape button to draw a hollow or filled freehand shape annotation on an image see page 5 32 for details There is no menu command equivalent to pressing this button Draw Text
21. details It is important to note that this does not change the information that has been captured just the way it is viewed 4 12 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Hints Saturation detection If you overexpose an image exposure time too long or iris too wide open the lighter parts of the image may be completely white and show no highlight details this is called saturation On the other hand if you underexpose an image exposure time too short or iris too small dark parts of the image may be all black without any shadow details The Show saturated areas button allows you to check whether an image contains any saturated areas areas of the image that are saturated to white are shown in red and any that are saturated to black are shown in blue Saturation mode is particularly useful when you are viewing a live image and adjusting the exposure time and iris settings to get the correct exposure in order to get the best results you should choose an exposure that avoids important parts of the image saturating and losing detail Note It is important to make sure that the image brightness and contrast controls are set to their default positions before adjusting the exposure time and iris settings see the note at the start of Adjusting display conditions page 5 13 for more details To check for image
22. for example to cut out bands To allow you to do this when Transilluminator is selected in the Lighting control you can override the door safety interlock for a live image Note You cannot override the safety interlock for Epi illumination To override the door safety interlock so that you can use the transilluminator with the door open 1 Display a live image in an Image window and select it 2 Open the Darkroom door Biolmaging Systems User Manual 5 11 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap 3 Select Transilluminator from the Lighting drop down list box the lighting graphic will show that the transilluminator is turned off when the door is open Note Steps 1 3 can be performed in any order 4 Take suitable precautions to protect yourself and all others present from UV light coming from the transilluminator For example fit the UV screen supplied with the Darkroom as follows a Open the Darkroom door fully and note the two support brackets at the left and right hand sides of the top edge of the door opening b Hold the transparent UV screen by its bottom edge in other words with the two holes away from you c Place the top edge of the UV screen onto the support brackets making sure that the pegs on the bracket are located in the holes in the screen Note You must not override the door interlock unless you take
23. freely on the desktop or dock it to another edge of the window To float the Histogram window 1 Move the pointer over the drag bars at the edge of the Histogram window Al 2 Drag the window away from the edge Note You can also float the Histogram window by double clicking on the drag bars it will be restored to the position it held when it was last floating 6 18 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The Histogram window To dock the Histogram window against an edge of the GeneSnap Application Window Drag the Histogram window by its title bar and drop it on the edge Note You can also dock the Histogram window by double clicking in its title bar it will be docked on the same edge as when it was last docked Using the Histogram window The Histogram window shows the distribution of intensities in the image in the selected Image window from 0 to fully saturated For 8 bit images non EDR GeneGenius MultiGenius and GeneWizard images this is 0 to 255 255 For 12 bit images non EDR ChemiGenius images this is O to 4095 And for 16 bit images GeneGnome and EDR images this is O to 65535 0 65535 You can use the Histogram window to ensure there is no loss of information because of saturation in the example above there is some loss of information because the distribution is cut off
24. providing powerful and time saving alternatives for full details of these and other features see Using GeneSnap Chapter 5 and the other reference chapters following it Biolmaging Systems User Manual 2 17 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneGenius MultiGenius or ChemiGenius 2 18 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneGnome This chapter gives a quick introduction to using your GeneGnome system taking you through the processes of starting up capturing an image and opening the image in GeneTools for analysis The final section of the chapter gives some hints on using GeneGnome There are other ways to carry out the operations described in this chapter providing powerful and time saving alternatives for full details of these and the many other features offered by GeneSnap see Using GeneSnap Chapter 5 and the other reference chapters following it Switching on To switch on the GeneGnome 1 Make sure the power leads are connected to a live supply 2 Turn on the main GeneGnome power switch this is a rocker switch just above the power input socket on the back of the GeneGnome 3 Press the processor on off button for a couple of seconds looking at the back of the GeneGnome this is a black
25. to prepare the system for capturing an image a 2 Press the Automatic exposure button in the Image Capture toolbox Note You can press the Automatic exposure button when the image is live or frozen 4 4 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Capturing an image from the camera Note These instructions have shown you how to capture an image using the settings saved in the Gel sample Configuration If you want to use other settings you can choose a different configuration or change the settings or options manually before carrying out Step 2 GeneSnap determines the correct exposure by grabbing a series of images starting with the minimum exposure and then with increasing exposures until an image is grabbed that has some saturated areas The exposure is then reduced by one step and the image captured and displayed in an Image window ready for further processing annotation or analysis as required The UV light inside the darkroom will be switched off automatically after the final exposure and the sample drawer will be released so that you can replace the sample Capturing an image from live video To capture an image manually from live video 1 Follow the procedure in Inserting the sample see page 4 3 to prepare the system for capturing an image 2 Ifa live image is not currently displayed press the green Free
26. 6 18 Contents 4 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Contents Docking and floating the Histogram window 2 o ee 6 18 Using the Histogram window 2 oa a e a 6 19 Histogram window cursors 2 2 ee a a 6 21 BIOWSED oe Ge a a we ee we de we eS 6 22 Toolbars 7 Displaying and hiding toolbars s eo s e tou asa ee 7 1 Arranging toolbars sosea moi gg ak ee a e MO a me Pe e 7 2 IMAG pa d oa PER a a o e a AD OS 7 2 Sharpen a bob ob ad AAA 7 2 SMOOTH cne a is GAG A eee a a de e en h a a a RAGS a 7 2 Speckle Correction MultiGenius Only o o a 7 2 INVETE n a a ad a AAA A 7 3 Flip Horizontal s g es a ew es a eG a ds we aa 7 3 Flip Vertical uso BG eae ee Ge Re A he 7 3 Define REGI N sa 2 4 4 2 Ae ee ee OA ee Bw ee ee eS 7 3 Crop to Regio pop x a Gee Ma a a A e a a A 7 3 ANNO eG ew ee ea ae eee ae ew ee Sa ee 7 4 Selec y AA Mca a a Gera te rs ee ok ake ee i K a 7 4 Draw Line e s 44 ocres ee A we we ee Be 7 4 Draw Rectangles 203 5 4 4 0 aces ga dh Pace eT Ee ee a eh ak 7 4 Draw Ellipse pos a lt actiua e 4h Be e be ae ohne e a Be A 7 5 Draw Freehand Shape e sos 4 2 ee amp Garde Be ee EO Be wes 7 5 Draw Text s e t saap a ee a a OS es wa 7 5 Draw AIOW eor e dake eo Se ke Ee OR we wo RS we PO a 7 5 Hollow Fill d Shapes s y s ane a iton iroa ahad ai a a Oe ee we 7 5 E 2 4 gaa a iag tau eee eee eee o
27. Choose Merge Annotation from the File menu to display the File List Selection dialog box Look in Annotations y al ex Files of type Merge with arm _ Cancel Lo This is a standard Windows Open dialog box similar to the Open dialog box displayed when you choose Open Image from the File menu see page 8 2 2 Use the dialog box to select the required annotation file 3 Press Open to close the dialog box and place the annotations on the image The annotations will be placed on the image as separate objects which you can move reshape delete and recolor independently 5 46 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The GeneSnap Application Window The GeneSnap Application window can contain the following components Menu bar The menu bar is always displayed see chapter 8 Menus for details Toolbars You can display or hide a variety of toolbars containing buttons and in one case a drop down list box for carrying out operations in GeneSnap Some tools are shortcuts for menu commands but others provide the only method of carrying out some operations See Chapter 7 Toolbars for how to hide show and arrange toolbars and for a description of each toolbar and toolbar button Status bar You can choose to display or hide the Status Bar at the bottom of the GeneSnap Application window The Status Bar displays a vari
28. Configurations with appropriate default settings for different types of analysis Any user on the PC can select any of the system default Configurations but they cannot edit or delete them Note You can change the settings from the system default Configuration values for use with an individual exposure but you cannot save the changes in the system default Configuration for use at a later time You can however save the changes in a user Configuration see the next paragraph In addition to system default Configurations you can create your own user Configurations When you create and save a user Configuration see Creating and saving Configurations page 5 2 it is saved on the PC for you individually you are identified by your login name see page 8 27 Each user on a PC has their own individual set of user Configurations which they can select and if required edit and resave at any time You cannot select a user Configuration saved by another user on the PC unless they have promoted it to be a system default Configuration see the next paragraph You can promote one of your own user Configurations to be a system default Configuration so that it can be used by other users logged in on the PC see Promoting Biolmaging Systems User Manual 5 1 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap a user Configuration page 5 4 for how
29. File menu see page 8 2 to open a previously saved image in a new Image window Pressing the Save button is equivalent to choosing Save Image from the File menu see page 8 4 to save the image or annotations in the selected Image window Biolmaging Systems User Manual 7 7 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Toolbars Print Pressing the Print button is equivalent to choosing Print from the File menu see page 8 14 to print the contents of the selected Image window Image Capture toolbox ku Press the Image Capture toolbox button to display the Image Capture toolbox if it has been hidden see page 6 2 for details There is no menu command equivalent to pressing this button Annotation toolbars g Pressing the Annotation toolbars button is equivalent to choosing Annotate from the Tools menu see page 8 26 to display or hide the annotation toolbars Annotate Color and Line Style Note Displaying the annotation toolbars automatically hides the Image toolbar Image toolbar S Pressing the Image toolbar button is equivalent to choosing Image from the Tools menu see page 8 25 to display or hide the Image toolbar Note Displaying the Image toolbar automatically hides the annotation toolbars Send to GeneTools Note The Send to GeneTools button is hidden if GeneTools is not installed on the PC ele Press the Send to GeneTools bu
30. Font list Click on a style for the text from the Font style list Select a font size from the Size list or type a value into the edit box If relevant select a script from the Script drop down list box some fonts come in different scripts such as Western Greek Turkish or Cyrillic Press OK to close the dialog box and return to the Caption dialog box Press OK in the Caption dialog box Note You can type the required text into the Caption dialog box when you close the dialog box the text will be placed on the image at the point you double clicked However you can also add text by typing directly on the image see the remaining instructions Note Changes to the default text orientation and font are not saved when you close GeneSnap the original defaults will be restored when you restart the program 5 38 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Placing annotations on an image 3 Move the pointer to the place you want to enter the text and click to place a flashing cursor on the image 4 Type the required text directly onto the image The Draw Text tool remains selected after you have added text ready for you to place some other text on another part of the image See Editing text annotations page 5 43 for how to edit text annotations Drawing an arrow To draw an arrow annotation on an image
31. Ge aOR ae a Ra BO ks 4 11 Logging IM e Ge e ad Ae ek A eo Ae Se ee a a et eG 4 12 Displaying the Image Capture toolbox n a a a a a a 4 12 Image display sos dci a na a a A 4 12 Saturation detection eo a es d mao e o 4 13 MOVINE OM 4 4 3 ao ed eee a o eS SS AAA 4 14 Using GeneSnap 5 Working with Configurations 2 o 5 1 User and system default Configurations o o o 5 1 Selecting a Config ation s lt lt s sos Be e A Sew A de ee A 5 2 Creating and saving Configurations s ao a a e o 5 2 Deleting a Configuration s s c s acora sasaa A erat 5 3 Promoting a user Configuration s s soa e cs are d ea Wobma saas 5 4 Capturing images from the camera o oo o a a ee 5 5 Capturing an image from live video not GeneGnome a aoao a a a a 5 5 Capturing a single image GeneGnome only a a a a 5 6 Capturing images using Series Capture 2 a a ee 5 7 Capturing images using auto exposure not GeneGnome ooa oaa 5 10 Using EDR Extended Dynamic Range not GeneGnome 5 10 Using the UV light with the Darkroom s door open a a 5 11 Adjusting display conditions e s s s a Toa sos wa e e aia i oe ae sa na d 5 13 Using the Image window display controls a a a a 5 13 Using the Histogram window to control the image display 5 14 Saving and loading image files 2 2 2 5 17 Loading imag
32. Press the Draw Text button to place a text annotation on an image see page 5 37 for details There is no menu command equivalent to pressing this button Draw Arrow Press the Draw Arrow button to draw an arrow annotation on an image see page 5 39 for details There is no menu command equivalent to pressing this button Hollow Filled Shapes Lad Press the Hollow Filled Shapes button to switch the Draw Rectangle Draw Ellipse and Draw Freehand Shape buttons between fill and hollow modes the Draw buttons show which mode is selected There is no menu command equivalent to pressing this button Biolmaging Systems User Manual 7 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Toolbars Color mimm Press a color button to set the default color for new annotations and change the color of the selected annotation if there is one There are no menu commands equivalent to pressing these buttons Line Style Press a style button to set the default line style for new annotations and change the line style of the selected annotation if there is one The line style affects lines arrows and the borders of hollow and filled shapes though the effect on filled shapes is only noticeable if you select the dashed or dotted line style There are no menu commands equivalent to pressing these buttons Zoom 22808 Zoom In A Pressi
33. Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Image 2 Press and hold down the mouse button then drag out the region that you want to crop to When you release the mouse button the region will be left selected shown by the drag handles at the corners and the middle of the sides and the pointer changes back to the selection pointer when it is not over a drag handle The region of interest is a selectable object which you can select at a later time to move reshape or delete see page 5 26 for details Crop to Region To crop the image to the region of interest B lt Choose Crop to Region from the Image menu If the Image window was in View Original mode when you chose the command a copy of the Original image will be cropped This Processed image will then replace any existing Processed image and the Image window will switch to View Processed mode If you switch back to View Original mode the original uncropped image will be displayed If the Image window was in View Processed mode the Processed image will be cropped When you crop an image there is a loss of image information Biolmaging Systems User Manual 8 37 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Menus Help Contents Index Using Help Show Wizard Change Wizard About GeneSnap Contents To display the Contents tab for the Help System
34. Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Index Copy 5 43 8 16 Copying annotations 5 43 Create new composite image 5 19 5 21 8 9 8 11 Crop to Region 5 26 7 3 8 37 Cropping an image 5 25 5 27 Cut 8 16 D Darkroom door Using the UV light with the door open 5 11 5 13 Define Region of Interest 5 25 7 3 8 36 8 37 Delete Configuration 5 3 8 30 Deleting annotations 5 42 Description 8 20 Display conditions 5 13 5 16 Document state 8 29 Door drawer icons 6 5 E Editing text annotations 5 43 5 44 EDR 6 11 See Extended Dynamic Range Ellipse annotation 5 31 5 32 7 5 Emboss 5 25 8 35 8 36 Engraving annotations 5 44 5 46 Exit 8 15 Export Image 5 45 8 6 8 8 Exporting images 5 44 5 46 Exposure time 2 15 6 8 Extended Dynamic Range 5 10 5 11 6 11 F Filled Shapes 7 5 Filter wheel control 6 12 Filter Wheel control 6 12 Flip Horizontal 5 25 7 3 8 35 Biolmaging Systems User Manual Index 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Index Flip Vertical 5 25 7 3 8 35 Focus controls 2 5 2 16 6 7 Framegrabber Installing A 3 A 4 A 6 Freehand shape annotation 5 32 5 36 7 5 Freeze Go live 6 5 6 6 G Gamma correction 5 13 5 14 6 16 6 17 GeneGenius Setting up 1 3 1 5 1 10 GeneGnome Connecting up 1 16 1 17 GeneSnap Exiting 8 15 Installing A 4 Starting 2 1 2 3 2 14 3 1 3 2 3 9 4 1 4 2 4 11 GeneSnap
35. USB socket on the back of the PC The USB plug can only be inserted one way round 3 Use the supplied braided cable with 25 way connectors on each end to connect the socket labelled DR1 on the back of the PC to the DR1 socket on the Darkroom 4 Use the supplied serial Darkroom cable with 9 pin connectors on each end to connect one of the Com port sockets on the back of the PC labelled Com 1 or Com 2 to the Com 1 socket on the Darkroom The cable can only be connected one way round as the connectors at each end are different 5 Connect power cables to the power sockets on the Darkroom on the back PC monitor and printer See Getting Started with GeneGenius MultiGenius and ChemiGenius Chapter 2 for how to switch on the system and use it to capture images 1 10 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ChemiGenius ChemiGenius2 Overview ChemiGenius is a comprehensive and fully automated gel documentation and analysis system designed specifically for chemiluminescence work though you can use it for normal gel work as well It achieves such outstanding results for chemiluminescence because it incorporates an advanced cooled CCD camera which is virtually noise free and thus allows very long exposures Images produced by ChemiGenius are crisp clear and noise free even for the faintest of bands
36. WwW White light pad Fitting in ChemiGenius 1 14 1 15 Fitting in GeneGenius 1 4 1 5 Fitting in MultiGenius 1 9 1 10 Windows open in GeneSnap 8 25 Z Zoom 1 1 7 7 Zoom controls 2 5 6 7 Zoom In 7 6 8 19 Zoom Out 7 6 8 19 Zoom to Fit 7 7 8 32 Zoom toolbar 7 6 7 7 8 26 Zooming Image windows 6 13 6 15 Biolmaging Systems User Manual Index 9 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Index Index 10 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com A rtisan Artisan Technology Group is your source for quality Technology Group new and certified used pre owned equipment FAST SHIPPING AND SERVICE CENTER REPAIRS WE BUY USED EQUIPMENT DELIVERY Experienced engineers and technicians on staff Sell your excess underutilized and idle used equipment TENS OF THOUSANDS OF at our full service in house repair center We also offer credit for buy backs and trade ins IN STOCK ITEMS www artisantg com WeBuyEquipment 7 EQUIPMENT DEMOS HUNDREDS OF InstraV ea REMOTE INSPECTION LOOKING FOR MORE INFORMATION MANUFACTURERS Remotely inspect equipment before purchasing with Visit us on the web at www artisantg com 7 for more our interactive website at www instraview com information on price quotations drivers technical LEASING MONTHLY specifications manuals and docume
37. and third image it will be superimposed on the first image s in its list box color 4 If you want to add one or more of the images as a negative inverting light and dark in the image check the corresponding Invert check box es 5 20 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Manipulating images 5 Check Create monochrome image if you want the composite image to be monochrome rather than color so that it appears similar to a normal captured image The composite image will be displayed in monochrome in the dialog box if you check the box 6 Check Balance maximum values in each color plane to weight the contributions of each image according to the maximum values in each see next paragraph for details of why you may want to do this If you do not select this option when GeneSnap creates a composite image it takes equal contributions from each component image However this can cause problems if one of the images is much lighter or darker than the other s or if the images are a mixture of EDR 16 bit and non EDR 8 or 12 bit images Balancing the maximum values in each color plane avoids these problems 7 Press OK to create the composite image The new composite image will be created and displayed in a new Image window You can apply any of GeneSnap s operations to the composite image in the same way as for a captured im
38. any already on the image in the selected Image window 1 Choose Merge Annotation from the File menu to display the File List Selection dialog box Look in E Annotations Al exi Files of type Merge with ann Cancel This is a standard Windows Open dialog box similar to the Open dialog box displayed when you choose Open Image from the File menu see page 8 2 2 Use the dialog box to select the required annotation file 3 Press Open to close the dialog box and place the annotations on the image The annotations will be placed on the image as separate objects which you can move reshape delete and recolor independently 8 8 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com File menu Create new composite image multiplexing Note The Create new composite image command is disabled unless two or more images are open in GeneSnap There are occasions when different parts of a gel may require different types of illumination For example you may have a chemiluminescence sample for which you need no illumination with a non chemiluminescent molecular weight standard track for which you need to use white light GeneSnap allows you to cope with this situation by capturing images under different illumination conditions and then combining them to form a composite image which can be analyzed in exactly the same way
39. being displayed press the red Freeze Go live button in the Image Capture toolbox to freeze the image Biolmaging Systems User Manual 2 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneGenius MultiGenius or ChemiGenius 3 Choose the Gel sample Configuration from the drop down list box in the Configuration bar at the top of the GeneSnap window Gel sample y Note This is one of the System default configurations supplied with GeneSnap The reason for choosing it here even if you are capturing a chemiluminescence image is that it is a convenient way to set options and parameters suitable for framing and focusing the image you can choose a different Configuration for carrying out the capture later See Working with Configurations page 5 1 to learn more about using Configurations 4 Open the Darkroom door 5 If you are going to use transmitted white light illumination remove the white light pad from its clips at the back of the Darkroom compartment and place it on the transilluminator 6 Place the gel centrally on the transilluminator or white light pad with the well line to the back leave the door open to allow light in so that you can frame and focus the image Note It is not essential to have the well line to the back since GeneTools will analyze gels in any orientation However gel images are normally shown with this orientat
40. bottom left hand corner of the front of the Darkroom is lit when the camera is showing or capturing for example during automatic or image series capture a live image To freeze a live image 1 Select the Image window displaying the live image p 2 Press the Freeze Go live button in the Image Capture toolbox Single exposure GeneGnome only To capture a single image in GeneGnome using the current exposure settings Press the Single Exposure button in the Image Capture toolbox The button turns red during the exposure and back to green once the exposure is complete Open drawer GeneGnome and GeneWizard only To open the sample drawer El Press the Open drawer button in the Image Capture toolbox The sample drawer is opened automatically when image capture is complete and when the GeneGnome or GeneWizard is switched off 6 6 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Image Capture toolbox Iris controls not GeneGnome or GeneWizard To open or close the camera lens iris in the Darkroom Press the iris open or iris close button in the Image Capture toolbox Note The iris controls the amount of light reaching the camera but also affects the depth of field of the lens the distance between the nearest and furthest points on the image that are in focus the more open the iris the smaller the depth
41. button will be enabled Press Open drawer button to release the drawer and then open it by pulling it towards you see note above 3 Place the sample in the drawer and push it closed until it is latched by the magnetic catch The buttons in the Image Capture toolbox will become enabled From this point there are two ways to proceed e Capture a single image with a preset exposure see the next section e Capture a series of images so that you can pick the best one see the next but one section Capturing a series of images Biolmaging Systems User Manual 3 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneGnome Capturing a single image To capture a single image 1 To set the exposure time a Click in the exposure time control in the Image Capture toolbox to select the hours minutes seconds or milliseconds section of the box 01m iis 000ms 1 b Type the new value over the numbers or click on the up or down spin arrow at the left hand end of the control to increase or decrease the number 01mElls 000ms Note You can also increase or decrease the exposure time by pressing the up or down arrow keys on the keyboard or if you are using a wheel mouse by turning the wheel c If required select another section hours minutes seconds or milliseconds and edit that number you can click on the scroll bars at the right h
42. by a light blue square Biolmaging Systems User Manual 5 33 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap 5 Move the pointer to the place you want the first line segment to end A wo Nowe Naat Nae Sm ts a Ml ta 6 Click to place the first line segment on the image A an Va Ne i ig Ml 1 5 34 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Placing annotations on an image 7 Repeat Steps 5 and 6 to add any further straight line segments required 8 To add a curved section to the line press and hold the mouse button down and drag out the section Biolmaging Systems User Manual 5 35 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap 9 To finish the freehand shape move the pointer to the place you want to put the last corner 10 Double click to place the corner and add two line segments to close the freehand shape When you have placed the freehand shape on the image the Draw Freehand Shape tool will still be selected so that you can place other freehand shapes on the image If you select the freehand shape annotation using the Select tool drag handles will appear where the edges change direction so that you can move or reshape the fr
43. display using two vertical red cursor lines 0 255 The picture above shows the Histogram window for an 8 bit image With a 12 bit ChemiGenius or 16 bit image GeneGnome or EDR the range is much wider for example The left hand cursor shows the image intensity that is displayed as black in the Image window and the right hand cursor shows the image intensity that is displayed as white Any parts of the image with intensities to the left of the left hand cursor or to the right of the right hand cursor will be displayed as black or white respectively 65635 Note For GeneGenius MultiGenius ChemiGenius and GeneWizard systems when the Histogram window is displayed the status bar shows the position of the left hand Black and right hand White cursors instead of the brightness and contrast For GeneGnome systems the status bar shows the position of the left hand Black and right hand White cursors even if the Histogram window is hidden Note If you adjust the brightness and contrast of the image display using the image controls with the Histogram window displayed you can see the cursors move in response to any adjustments you make to the image controls Biolmaging Systems User Manual 5 15 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap In the previous examples the cursor lines lie outside the actual distribution so no parts of t
44. each new image if you want the results to be cumulative each new image is the result of adding the new exposure to the previous image in the series Uncheck Add contents of previous images to each new image if you want all images in the series captured with the set exposure 5 Check Use same exposure for all images in series if you want to set a single exposure for all images Note If you check both Use same exposure for all images in series and Add contents of previous images to each new image the exposure time for the first image will be the set exposure for the second image the effective exposure time will be 2x the set exposure for the third it will be 3x the set exposure and so on Uncheck Use same exposure for all images in series if you want to set a separate exposure for each of the images Biolmaging Systems User Manual 4 7 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneWizard 6 If you have checked Use same exposure for all images in series you can adjust the exposure time as follows a Click in the exposure time control to select the hours minutes seconds or milliseconds section of the box 00m Hs 000ms b Type the new value over the numbers or click on the up or down spin arrow at the left hand end of the control to increase or decrease the number 00m Es 000ms Note You can also increase or decrease the ex
45. image information The effect of sharpening an image is to increase the fine detail in the image the high spatial frequencies by adding the difference between the original image and a locally averaged version Biolmaging Systems User Manual 8 33 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Menus Smooth Bs Invert To smooth the image make the boundaries between areas less sharp in the selected image window Choose Smooth from the Image menu If the Image window was in View Original mode when you chose the command a copy of the Original image will be smoothed This Processed image will then replace any existing Processed image and the Image window will switch to View Processed mode If you switch back to View Original mode the original unsmoothed image will be displayed If the Image window was in View Processed mode the Processed image will be smoothed If required you can smooth a Processed image repeatedly When you smooth an image there is a loss of image information The smooth operation is carried out by calculating a local average for each pixel in the image To invert the image display reverse black and white for a monochrome image or replace colors by their complementary colors for a color image Choose Invert from the Image menu If the Image window was in View Original mode when you chose the command a copy of the Original image wil
46. is how the white light pad should be located when you are using it If you want to use the transilluminator you can stow the white light pad out of the way in the Darkroom without disconnecting it To do this lift the white light pad up at the front until it is nearly vertical and then slide it down into the clips at the back of the Darkroom Connecting up the System To connect up a complete ChemiGenius system 1 Connect the monitor keyboard and mouse to the labelled sockets on the back of the PC Note At this stage you may want to connect the PC to the power and turn it on to check that it is working correctly If you do this the GeneSnap log on dialog box will be displayed after Windows has opened press Cancel to close GeneSnap When you are satisfied that the PC is working correctly close down Windows switch off the PC and disconnect it from the power supply before proceeding to the next step 2 Connect the thermal printer to a USB socket on the back of the PC The USB plug can only be inserted one way round 3 Use the supplied Firewire cable to connect the labelled socket on the camera control box which can be accessed through the back of the Darkroom to any of the 3 Firewire sockets on the PC s Firewire card which can be accessed through the back of the PC 4 Use the supplied serial Darkroom cable with 9 pin connectors on each end to connect one of the Com port sockets on the back of the PC labelled Com 1
47. ke oe Ae ee 8 5 ClosetlMages a2 eA ae A A be ee ee a 8 6 Export Images 4 2 acacia se Bh a Oa Be a a AE 8 6 Merge Annotation vox sos ser wad ea e Ge Soe a we ae Ss 8 8 Create new composite image multiplexing 2 o 8 9 Printer SETUP vado GR See we e ROD al a were ae ae Ge ale 8 12 Report Settings sys d s a Sido wok Ee BORE we Wa me Ga e gtd 8 13 PEE REVIEW axa een ae ee Ge GN eee ES eS a et ee ae Ge 8 13 PRING gs as eh le be ego a Se GR Be A ees 8 14 Most recently used files p atop a s cs sae ew aw a a 8 15 PG sds tase Ge arbi age ENG A tanh Bp nae ads RE ye Bo he ee aR Ree a Be Bote Bones 8 15 Edita chee are hee dk A oe ee a eee Bem ee a Be Be 8 16 CUE sg eni ao ran Ake ae A he ee en a ae ee Be Ae a 8 16 COPY A sue bird arde add 8 16 Paste se ek em a e a ee oe a 8 16 UNdO ne pb de Bea bea EE eae SAA Ee Ee 8 16 MEW amp a i doa he amp Ep e Ad a eS Stee Se 8 17 AANMOLALIONG dd o eB wad a ew Ew a 8 17 Histograms avi Qu ois ka oo ak ee we ee a OG eG 8 18 GNA OM LIVE s gsang Ae Be Bee ew Soe oe e OR Ge a 8 18 Normal lll adas a pomada VA aed et Gk e ee fk Be amp 8 18 LOOM oo iaa EE BO a Bo Ah a 8 19 Contents 6 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Contents ZOOM QU vos ra ar ia BEd Be ae ea Wh ee eh dy 8 19 View Original gog ash ang eet Ge amp ace Be be mae Sa ale 8 19 View Processed z a o ace oi e
48. left hand pane in Windows Explorer to select the folder containing the required image 6 22 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Browser The right hand pane in the Browser will show a preview of all the images in the selected folder 2 Double click on the image that you want to open Biolmaging Systems User Manual 6 23 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The GeneSnap Application Window 6 24 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Toolbars The GeneSnap Application window has the following toolbars Image for processing the image for presentation purposes to make it sharper smoother less speckled inverted negative image flipped or cropped Annotation toolbars for adding and setting the properties of annotations There are three annotation toolbars which are displayed or hidden together e Annotate for adding text and graphics as an overlay to the image e Color for setting the color of new or existing annotations e Line Style for setting the width style of lines used for a new or existing line arrow or hollow or filled shape annotations Zoom for displaying a magnified or reduced view of the image or resetting it to the
49. modes page 6 17 for further information View Processed To switch the selected Image window to View Processed mode Choose View Processed from the Image menu The command is disabled if there is no Processed image associated with the selected Image window See Original and Processed View modes page 6 17 for further information Biolmaging Systems User Manual 8 19 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Menus Properties To view edit the properties of the image in the selected Image window 1 Choose Properties from the View menu to display the View Properties dialog box View Properties The Description page shows the unique image ID number the time and date it was captured and by whom you cannot change this information 8 20 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com View 2 Click on the User Fields tab to display the User Fields page View Properties Enter or edit text in the User Field boxes to document the image the text will be stored with this individual image and can be printed out with the image in a report Biolmaging Systems User Manual 8 21 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Menus 3 Click on the Capture tab to di
50. or Com 2 to the Com 1 socket on the Darkroom The cable can only be connected one way round as the connectors at each end are different 5 Connect power cables to the power sockets on the Darkroom on the back PC monitor and printer See Getting Started with GeneGenius MultiGenius and ChemiGenius Chapter 2 for how to switch on the system and use it to capture images Biolmaging Systems User Manual 1 15 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Introduction and Initial Setup GeneGnome Overview GeneGnome is a comprehensive and fully automated documentation and analysis system designed specifically for chemiluminescence work It achieves such outstanding results for chemiluminescence because it incorporates an advanced 16 bit cooled CCD camera which is virtually noise free and thus allows very long exposures The fact that it is 16 bit means that it has a much wider dynamic range than other camera based systems on the market in fact it has a wider dynamic range than film Images produced by GeneGnome are crisp clear and noise free even for the faintest of bands over extended exposures Standard GeneGnome systems are supplied with GeneGnome Darkroom fitted with a 16 bit cooled CCD camera with prefocused f0 8 fixed lens Built in PC fitted with a framegrabber keyboard and mouse Flat screen monitor GeneSnap acquisition software GeneTool
51. original size or setting autosizing mode Standard for creating a new Image window showing the camera image loading saving or printing an image file displaying the Image Capture toolbox displaying or hiding the annotation and Image toolbars displaying or hiding the Histogram window starting GeneTools to analyze an image or displaying on screen Help for a window component Configuration for choosing which Configuration to use Displaying and hiding toolbars You can choose to hide or display the Zoom and Standard toolbars independently by choosing the command in the Tools menu with the same name as the toolbar The command is checked in the menu when the toolbar is displayed You can also choose commands in the Tools menu or press buttons in the Standard toolbar to display either the Image toolbar or the annotation toolbars Annotate Color and Line Style The Configuration toolbar is always displayed Biolmaging Systems User Manual 7 1 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Toolbars Arranging toolbars All the toolbars are displayed in the toolbar area below the menu bar at the top of the GeneSnap Application window You can drag the toolbars by the drag bars at their left hand edge to move or rearrange them except that the Image and annotation bars always appear below the other toolbars Image BE PS i BS Note The Speckle Correction
52. part of it Note Only certain values of exposure time are allowed if you type a non allowed value directly into the box it will be corrected to the next allowed value 4 Press the red Freeze Go live button in the Image Capture toolbox The image will be captured frozen in the Image window ready for further processing annotation or analysis as required The UV light inside the darkroom will be switched off automatically after the final exposure and the sample drawer will be released so that you can remove the sample Capturing a series of images To capture a series of images from a sample 1 Follow the procedure in Inserting the sample see page 4 3 to prepare the system for capturing an image 4 6 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Capturing an image from the camera yoo 2 Press the Image series button in the Image Capture toolbox to display the Series Capture dialog box Number of images in series 5 IV Add contents of previous images to each new image IV Use same exposure for all images in series Exposure control Exposure time E 00m 05s 000ms ll 3 Set the number of images you want to capture in the series by clicking on the arrow buttons next to the Number of images in series spin box you can choose from 1 to 100 inclusive 4 Check Add contents of previous images to
53. push button switch at the top right hand corner of the back panel 4 Turn on the monitor The GeneGnome will take a little time to start up while it loads Windows and then GeneSnap Biolmaging Systems User Manual 3 1 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneGnome When GeneSnap starts up the first time you will be asked to log on GeneSnap User name 1 Type in your name If you have opened GeneSnap before and entered your name you will be able to select it from the drop down list 2 Press OK to open GeneSnap The main GeneSnap Application window see Chapter 6 will open with the Image Capture toolbox displayed on its left hand side E 00m 00s 040ms 3 2 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Capturing an image from the camera Capturing an image from the camera To prepare to capture an image 1 Prepare the sample 2 If you have just switched on the GeneGnome the sample drawer at the bottom of the GeneGnome will be unlatched and you should open it by pulling it towards you Note Keep hold of the drawer and pull carefully to avoid pulling the drawer completely out of the GeneGnome If the sample drawer is closed this will be shown on the graphic in the Image Capture toolbox and the Open drawer
54. saturation Press the Show saturated areas button in the image control bar at the right hand edge of the image window When saturation mode is on any areas of the image that are saturated to white are shown in red and any that are saturated to black are shown in blue This enables you to determine whether any details in important areas of the image are being lost because of saturation Note It is important to make sure that the image brightness and contrast controls are set to their default positions before using saturation mode to decide whether you need to adjust the exposure time see the note at the start of Adjusting display conditions page 5 13 for more details When saturation mode is on the Show saturated areas button is shown as depressed To switch saturation mode off Press the Show saturated areas button again You can also judge the degree of saturation by displaying the Histogram window Biolmaging Systems User Manual 4 13 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneWizard To display the Histogram window dl Choose Histogram from the View menu to view the Histogram window 255 Provided the distribution lies within the range of the histogram without saturating at either end you will be able to carry out a quantitative image analysis with confidence You can also use the Histogram window to adjust th
55. selected image window e The exposure time Image Capture toolbox To display the Image Capture toolbox if it has been hidden rer Press the camera button in the Standard toolbar Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Image Capture toolbox The contents of the Image Capture toolbox depends on the system GeneGenius MultiGenius ChemiGenius GeneGnome GeneWizard No live image Live image displayed displayed 7 ene 00m 00s 040ms 00m 00s 040ms a s cs Epi long wave uy Epi long wave uy E 00m 00s 040ms 00m 00s 040ms Transilluminator ro E Max sensin y Mas senstiy E EtBr UV EtBr UV y Note The first two pictures show the Image Capture toolbox for ChemiGenius the sensitivity resolution drop down list box does not appear for GeneGenius or MultiGenius or GeneGnome or GeneWizard Note The Automatic Exposure button is permanently disabled and the EDR check box and lighting controls are permanently hidden for GeneGnome The Filter control is permanently hidden for GeneGnome and GeneWizard and for GeneGenius systems without the filter wheel option Biolmaging Systems User Manual 6 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The GeneSnap Application Window Docking and floating the Image Captu
56. selecting the current Configuration 1 Choose Save Configuration As from the Extras menu to display the Save Configuration dialog box Current User Configurations wave EPI Save As Short wave EPI Description Note The list box at the top of the dialog box shows all your Current User Configurations the list does not include any system default Configurations on your PC see Promote Configuration page 8 31 for more information about system default Configurations 2 The Save As box shows the name of the current Configuration or Type new config name here if the current Configuration is a system default Configuration Either Leave the existing name unchanged if you want to update the current Configuration to the current capture settings Biolmaging Systems User Manual 8 29 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Menus Or Enter a new name if you want to create a new Configuration with the current capture settings Note If the original Configuration was a system default Configuration you must enter a new name you cannot save changes to a system default Configuration 3 Enter or edit the Description to document the Configuration 4 Press OK to close the dialog box and save the changes to the existing Configuration or create a new user Configuration with the current capture settings See Working with Configuratio
57. techniques and how to add annotations Biolmaging Systems User Manual 1 1 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Introduction and Initial Setup Chapter 6 The GeneSnap Application Window describes the layout of the program interface and shows you how to work with the Image Capture toolbox Image windows the Histogram window and the Browser Chapter 7 The Toolbars describes some general features of working with toolbars and then provides instructions for using each of the tools Chapter 8 Menus describes each of the menus in turn with instructions for using the commands they contain Finally an appendix shows you how to install the framegrabber board and all necessary software in a PC if you have not purchased a complete Biolmaging System GeneGenius Overview GeneGenius is a comprehensive and fully automated gel documentation and analysis system It features some extremely advanced concepts in image acquisition and processing and is ideal for laboratories working with all types of gel media including DNA gels protein gels and autoradiographs Complete GeneGenius systems are supplied with e SYNGENE Darkroom fitted with an 8 bit 16 bit performance provided by EDR CCD camera e Motorized zoom lens with close up filter e UV Transilluminator with illuminated area of 20cm x 20cm optional 20cm x 30cm version e White light pad e Epi white light il
58. three images and so on 7 Press OK to confirm your selections close the dialog box and start the image capture The captured images will be shown in separate Image windows so that you can select the best one for further analysis and or printing Biolmaging Systems User Manual 5 9 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap Capturing images using auto exposure not GeneGnome Note The auto exposure procedure may take an unacceptably long time for images requiring long exposures In particular you should not use auto exposure to capture chemiluminescence images Note You cannot perform an EDR exposure when using auto exposure the Automatic exposure button is disabled in the Image Capture toolbox if EDR is selected To grab a single frame using the current lens settings and an automatically determined exposure aj Press the Automatic exposure button in the Image Capture toolbox GeneSnap determines the correct exposure by grabbing a series of images starting with the minimum exposure and then with increasing exposures until an image is grabbed that has some saturated areas The exposure is then reduced by one step and the image captured and displayed in an Image window if there is an Image window connected to the camera the captured image will be displayed in it otherwise a new Image window will be opened to display the c
59. to the minimum time see Step 8 in Framing and focusing the image see page 2 3 for how to set the iris GeneSnap determines the correct exposure by grabbing a series of images starting with the minimum exposure and then with increasing exposures until an image is grabbed that has some saturated areas The exposure is then reduced by one step and the image captured and displayed in an Image window ready for further processing annotation or analysis as required The light inside the darkroom will be switched off automatically after the final exposure to minimize any damage to the sample Capturing an image from live video You can use this capture procedure in any of the systems considered in this chapter and GeneWizard but not GeneGnome The following instructions use transmitted white light illumination as an example but you can use the same technique with any type of illumination However since you can only display live images when the exposure is set to less than 5 seconds it cannot be used for chemiluminescent samples To capture an image manually from live video 1 Follow the procedure in Framing and focusing the image see page 2 3 to prepare the system for capturing an image 2 6 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Capturing an image Note This example uses transmitted white light illumination so make sur
60. use the complementary colors for a color image Choose Invert from the Image menu There is no loss of image information when you invert an image 5 24 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Manipulating images Embossing an image GeneSnap allows you to produce a 3 D embossed view of the image emphasizing the boundaries between regions To emboss the image Choose Emboss from the Image menu When you emboss an image there is a loss of image information Flipping an image To flip an image vertically swap top and bottom or horizontally swap left and right Choose Flip Vertical from the Image menu Pa Choose Flip Horizontal from the Image menu There is no loss of image information when you flip an image Cropping an image To crop an image to a region of interest E 1 Choose Define Region of Interest from the Image menu When you move the pointer over the image it changes to a cross hair Biolmaging Systems User Manual 5 25 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap 2 3 B lt 4 Press and hold down the mouse button then drag out the region that you want to crop to If required move or reshape the region of interest after you have placed it on the image see instructions later in this section
61. will still be selected so that you can place other lines on the image If you select the line annotation using the Select tool drag handles will appear on the ends of the line so that you can move or reshape the line Note You can select the Select tool when the Draw Line tool is selected by pressing the Select button on the Annotate toolbar Biolmaging Systems User Manual 5 29 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap Drawing a rectangle To draw a rectangle annotation on an image 1 Choose whether to draw a filled or hollow rectangle press the Hollow Filled Shape button if the Draw Rectangle button shows the wrong sort of rectangle or CI 2 Press the Draw Hollow Rectangle button Press the Draw Filled Rectangle button 3 Move the pointer to the position where you want to place one corner of the rectangle When the Draw Rectangle tool is selected the pointer changes to a cross hair when it is over the image 4 Press and hold down the mouse button then drag the pointer to the opposite corner of the rectangle 5 30 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Placing annotations on an image When you have placed the rectangle on the image the Draw Rectangle tool will still be selected so that you can place other rectangles on t
62. without the prior permission of the copyright owner Published by SYNGENE a division of Synoptics Limited Synoptics Limited 2003 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Contents Introduction and Initial Setup 1 Introductions sens a e anra a A A Ge Ge wl ee We a 1 1 GeneGenius 2 g a Gk ao ee A wk a gh as 1 2 COVEIVICW 2 2 es Se dh er A A ee a a a A 1 2 Setting up the Darkroom s 2 s s ss sco me dania Re A A 1 3 Connecting up the System s w s s esa w ea a e a 1 5 MultiGeniuss s a 6 3 4 6 boca ee a bed 1 6 OVERVIEW eo aa ae a da eo ae A oe ae ee ee ee Se e 1 6 Setting p the DDN s s ca ie AM a be el a OE ee SSS 1 7 Connecting up the System s s u roeie w ae Pa e e u aa a 1 10 Ch emiGenius2 a aopa RE ea eae e o a aia a 1 11 OVETVICW SS oa de iS BES ae Gs ah ee ipa A Ge de ves a o ey a 1 11 Setting up the DamkrOOMia se a od eo a oe oP a EWR dk a ERS 1 12 Connecting up the System sas 2 2 a e 1 15 GENEGMOM S 2k a We a eR ae Ae be aoe ES ae at Sw ee 1 16 Y so b Sa ace ge aca a Rei oe AP a ar Be a ee as ae amp a eR ee 1 16 Connecting up the System as a co ew h a a a a 1 16 GeneWizard e s e i 2 ee a Shade a Aa Boom has 1 17 OVEIMIEW o iii e i e he we ae a eS Be ee eed 1 17 Connecting up the System a a oa a
63. your selections close the dialog box and start the image capture The captured images will be shown in separate Image windows so that you can select the best one for further analysis and or printing Biolmaging Systems User Manual 3 7 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneGnome Analyzing the image The next step after capturing an image is to analyze it to do this you will use SYNGENE s GeneTools To start up GeneTools to analyze the image in the selected Image window it Fa 1 Press the Send to GeneTools button A standard Windows Save As dialog box will open so that you can save the image file Save As 1 1x Saven E maes El al ci Image1 sad Image2 sgd Image3 sgd Image4 sgd Image5 sgd Image6 sgd File name Image sgd i E Save as type GeneSnap sgd ld Cancel Zi Select a folder to hold the image file from the Save in drop down list and the file list box below it 3 Enter a name for the image file in the File name box 4 Press Save to save the image with the new name Once you have saved the image GeneTools will open with the image loaded ready for you to analyze it see your GeneTools documentation for how to use GeneTools 3 8 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Hints Hin
64. 11 7 8 7 9 Sensitivity resolution 6 11 Sharpen 5 23 5 24 7 2 8 33 Show Histogram Window 7 9 Show Wizard 8 39 Single exposure GeneGnome 6 6 Smooth 5 23 5 24 7 2 8 34 Software installation A 1 A 3 A 4 A 6 Speckle Star Field correction 5 24 After capture 7 2 7 3 Standard toolbar 7 7 7 9 8 26 8 27 Status Bar 6 1 6 2 8 23 Switching on ChemiGenius 2 1 2 3 GeneGenius 2 1 2 3 GeneGnome 3 1 3 2 GeneWizard 4 1 4 2 Biolmaging Systems User Manual Index 7 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Index MultiGenius 2 1 2 3 System default Configurations 5 1 5 5 8 29 8 31 T Take snapshot only 8 29 Text annotation 5 37 5 39 7 5 Text annotations Editing 5 43 5 44 Tile Horizontal 8 24 Tile Vertical 8 24 Toolbars 6 1 7 1 7 10 Arranging 7 2 Showing hiding 7 1 7 8 8 25 8 27 Transilluminator Fitting in ChemiGenius 1 13 1 14 Fitting in GeneGenius 1 3 1 4 Fitting in MultiGenius 1 8 1 9 U Undo 8 16 8 17 Unique image ID 8 20 User Configurations 5 1 5 2 5 4 5 5 8 29 8 31 User Fields 8 21 User name 8 27 Using Help 8 38 UV light Using with the Darkroom s door open 5 11 5 13 UV Safety Override 5 11 5 13 V View Original 5 23 5 44 6 17 8 19 View Processed 5 23 5 44 6 17 8 19 Index 8 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Index
65. Application Window 6 1 6 24 GeneTools 2 13 3 8 4 10 4 11 7 8 7 9 Installing A 1 A 3 GeneWizard Connecting up 1 18 Grabber support Installing A 4 A 6 Grid on Live 8 18 H Help 7 9 8 38 8 39 Histogram window 2 17 3 10 3 11 4 13 4 14 5 14 5 16 6 1 6 18 6 24 7 9 8 18 Controlling the image display 5 14 5 16 6 21 Cursors 6 21 Docking and floating 6 18 6 19 Showing and hiding 6 18 Using 6 19 6 21 Hollow Filled Shapes 7 5 Index 4 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Index Image Capture toolbox 6 1 6 12 7 8 Displaying 2 14 3 9 4 12 6 2 6 3 Docking and floating 6 4 Image controls 5 13 5 14 6 16 6 17 Image file Closing 8 6 Loading 5 18 5 19 Saving 5 17 5 18 8 4 8 6 Image series 6 9 Image toolbar 5 22 5 23 7 2 7 3 7 8 8 25 8 26 Image windows 6 1 6 12 6 18 Closing 8 6 8 25 Opening new 8 2 Scrolling 6 13 6 15 Selecting 6 13 Zooming 6 13 6 15 Index 8 38 Help 8 38 Initial Acquire State 8 28 8 29 Invert 5 24 7 3 8 34 Iris controls 2 5 6 7 L Lighting control 6 9 6 10 Line annotation 5 28 5 29 7 4 Line Style toolbar 5 28 7 6 7 8 8 26 Logging in 2 14 3 9 4 12 M Media Key A 1 Menu bar 6 1 Menus 8 1 8 40 Merge Annotation 5 44 5 46 8 8 Monochrome image controls 5 13 5 14 6 16 6 17 Most recently used files 8 15 Biolmaging Systems User Manual Index 5 Artis
66. Practice Biolmaging Systems User Manual 8 11 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Menus Printer setup To choose a new printer or change the settings for the existing one 1 Choose Printer setup from the File menu to display the Print Setup dialog box Print Setup 21x m Printer Name HP LaserJet 41000 TN PCL6 Properties Status Default printer Ready Type HP LaserJet 4100 PCL 6 Where Ipt Comment m Paper Orientation gt Size A4 E Portrait Source Plain C Landscape Cancel 2 To select a different printer choose it from the Name drop down list box The fields below the Name box show properties of the selected printer 3 Press Properties to display a dialog box allowing you to choose options for the selected printer The options available depend on the printer see your printer documentation for details 4 Choose the paper Size and Source to use from the drop down list boxes The options available depend on the printer see your printer documentation for details 5 Click on the Landscape or Portrait radio button to choose the paper orientation the graphic in the Orientation box illustrates the selected orientation 6 Press OK to save the settings and close the dialog box 8 12 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaran
67. Save in drop down list and the file list box below it 4 Enter a name for the exported image or annotations file in the File name box 5 For 8 bit images non EDR GeneGenius MultiGenius and GeneWizard or 12 bit image non EDR ChemiGenius check Convert to 16bit if you want the image saved as a 16 bit image The image will be exported as a 16 bit tiff file 6 For 16 bit images GeneGnome and EDR images check Convert to 8bit if you want the image saved as an 8 bit image 7 Select the format for saving the file from the Save as type box you can save images in a wide variety of image formats or just save the annotations in a ann file you will be able to add the saved annotations to images in GeneSnap at a later time using Merge Annotation Biolmaging Systems User Manual 8 7 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Menus 8 For an image export check Engrave Annotation if you want to export the image with any annotations leave it unchecked if you want to export the image only Note If you choose to export the image with annotations the annotations will become part of the exported image engraved and the underlying parts of the original image will be permanently obscured in the exported image 9 Press Save to save the image or annotations with the new name Merge Annotation To add the annotations saved in an annotation file to the annotations if
68. Selecting 5 41 Showing and hiding 5 28 8 17 8 18 Arrange Icons 8 24 Arrow annotation 5 39 5 41 7 5 Automatic exposure 2 5 2 6 4 4 4 5 6 8 Autoscale on capture 8 32 Brightness 5 13 5 16 6 16 6 17 Biolmaging Systems User Manual Index 1 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Index Browse 6 22 6 24 8 3 8 4 Browser 6 1 6 22 6 24 8 3 8 4 C Camera Fitting in ChemiGenius 1 12 1 13 Fitting in MultiGenius 1 7 Capture properties 8 22 Capturing images 3 3 3 7 4 3 4 9 5 5 5 11 Auto exposure 2 5 2 6 4 4 4 5 5 10 From live video 2 6 2 7 4 5 4 6 5 5 5 6 GeneGenius MultiGenius ChemiGenius 2 3 2 12 GeneGnome 3 3 3 7 GeneWizard 4 3 4 10 Series Capture 2 8 2 11 3 5 3 7 4 6 4 9 5 7 5 9 Single images using GeneGnome 3 4 5 6 Using EDR 2 12 4 10 5 10 5 11 Cascade 8 24 Change Wizard 8 39 ChemiGenius Setting up 1 12 1 15 Close All 8 25 Close Image 8 6 Color toolbar 5 28 7 6 7 8 8 26 Color wash palette 5 13 5 14 6 16 6 17 Composite image 5 19 5 21 8 9 8 11 Configuration toolbar 7 9 7 10 Configurations 5 1 5 5 Creating 5 2 5 3 Deleting 5 3 8 30 Promoting 5 4 5 5 8 31 8 32 Saving 5 2 5 3 8 29 8 30 Selecting 5 2 System default 5 1 5 5 8 29 8 31 User 5 1 5 2 5 4 5 5 8 29 8 31 Contents Help 8 38 Context sensitive Help 7 9 Contrast 5 13 5 16 6 16 6 17 Index 2 Biolmaging Systems User Manual Artisan Technology Group
69. Zoom Out Close Press Next Page to preview the next page if there is one Print Nevt Rage Prey Rage Press Prev Page to preview the previous page if there is one Press Two Page One Page to change between previewing multiple page reports two pages or one page at a time Press Zoom In and Zoom Out to change the magnification of the preview alternatively click the left respectively right mouse button Press Close to return the Image window to normal mode Press Print to send the printout to the printer and return the Image window to normal mode To print the contents of the selected Image window 1 Choose Print from the File menu to display a standard Windows Print dialog box Print 21x m Printer Name HP LaserJet 4100DTN PCLE Properties Status Default printer Ready Type HP LaserJet 4100 PCL 6 Where Ipt4 Comment JT Print to file gt Print range Copies 3 All Number of copies fi a Pages from 1 to Selection Rog T Collate Cancel 2 If required choose a different printer from the Name drop down list box 8 14 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com File menu Press Properties to display a dialog box allowing you to set options for the selected printer The options available depend on the specific printer selected see you
70. a ee ee ae ae t a 7 6 Bine AA Be ae ae Sk gee ba ee a a a he ae S 7 6 ZOOM xis a cg A seria AE ee ee ee es AA a 7 6 ZOOM Ms a oe sco as Rh he we BY Bos Aa a aE Be e A BO a a 7 6 ZOOM QUE i 4 4 eG ERE REDRESS EEE REPRE SE ROHR S 7 6 Zoomed 84 4 6 o h2 6 5 baw OER ERASE EEE RAGGA 7 7 LOODETE TIE 1 006 ye yc e A Re ee we AE Ge be ER Bn one 84 8 7 7 Standard ece ele abe eR ed ee eRe ee eee eee ea 7 7 NEWS 2 de ie Bd Ae Se we OG A OS A Gs ek we 84 a N 7 7 ODEN aS 2 a Ge Se ee oe oe ee ee we ee ee oe at eu 7 7 SAVES foe Gk Ge Re ew eG HR RDG Pa we Re ewe we a 7 7 Biolmaging Systems User Manual Contents 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Contents PRES cae fe ah a ne Gy Bee a a Me ee ae ee a 7 8 Image Capture toolbox e s s p sna a a e 7 8 Annotation toolbars 2 e 7 8 Image toolbar o s i ame ba eee e ee EEE EL EEE BS 7 8 Send to GeneTools o o sce cos oew wa erea ha e a a e 7 8 Show Histogram Window oaoa a a 7 9 Context sensitive Help s x o s aos alasa e pa paa e ea 7 9 Configurations s as s Ble Ge aks a a eee GG we N a 7 9 Menus 8 File MEU cios Pos bot aw bE EG LoL DEES ABE DE ERO 8 1 New Images i eon iain amp amp Baa e o BE ee ee ea AA e i 8 2 Open Image x sos w 4 be a ee wae Be a eee we 8 2 BROWSE Go e sopaya a Oe ee Sw ee a 8 3 Save IMAGE si aen e Gh A ae ace Gl deg ht Ge WAG ao a el A es 8 4 Save IM BE AS n aoa se AA eee
71. adequate precautions to ensure that the UV light cannot enter your eyes or anyone else s you must wear the appropriate protective eye or face shield or use the UV shield provided 5 Double click on the lighting graphic in the Image Capture toolbox to display the UV Safety Override dialog box UY Safety Override Eg Caution You are overriding the UV safety Do you really want UY light on J with door open Le 6 Press Yes to turn the transilluminator on 5 12 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Adjusting display conditions The lighting graphic in the Image Capture toolbox will light up to show that the transilluminator is on You can repeat Steps 5 and 6 to turn the transilluminator off again The door safety interlock will be re engaged if you freeze the image or shut the Darkroom door Adjusting display conditions Note The adjustments described in this section only affect the display of the images they have no effect on the actual image values This may cause problems when you are setting the iris or exposure time to get the best exposure For example if you increase the brightness of the image display of a correctly exposed image the light parts of the image will get lighter and eventually become saturated and be shown in red if the Show saturated areas button is depressed H
72. age In particular you can save the composite image and analyze it in GeneTools Note Image files created using the Create new composite image command do not satisfy the conditions required for Good Laboratory Practice this fact is noted in the composite image s Capture properties see Properties page 8 20 for how to view image properties Manipulating images Note This section describes how to process images in a number of ways for presentation purposes In order to maintain good laboratory practice the processing is performed on a copy of the original image and when you save the image both the original and processed images are saved in the image file If you load the image file into GeneTools for analysis the original image will be analysed not the processed one Biolmaging Systems User Manual 5 21 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap This section shows you how to use GeneSnap to e Sharpen or smooth the image see page 5 23 e Apply speckle correction see page 5 24 e Invert the image swap black and white on a grey scale image or use the complementary colors on a color image see page 5 24 e Emboss the image see page 5 25 e Flip the image horizontally or vertically see page 5 25 e Crop the image see page 5 25 Note GeneSnap does not contain a function allowing you to ro
73. age by more than a threshold value which is 64 by default it is replaced by the average value There is no menu command equivalent to pressing this button Pressing the Invert button is equivalent to choosing Invert from the Image menu see page 8 34 to invert the image display reverse black and white for a monochrome image or replace colors by their complementary colors for a color image Flip Horizontal A Pressing the Flip Horizontal button is equivalent to choosing Flip Horizontal from the Image menu see page 8 35 to flip the image from left to right Flip Vertical Pressing the Flip Vertical button is equivalent to choosing Flip Vertical from the Image menu see page 8 35 to flip the image from top to bottom Define Region Pressing the Define Region button is equivalent to choosing Define Region of Interest from the Image menu see page 8 36 to define a region of the image to crop to Crop to Region Pressing the Crop to Region button is equivalent to choosing Crop to Region from the Image menu see page 8 37 to crop the image to the region of interest defined using Define Region of Interest in the Image menu see page 8 36 or the Define Region button Biolmaging Systems User Manual 7 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Toolbars Annotate ki Ni Sar Note The rectangle ellipse and freehand shape icons may appear hollow
74. all images in the series captured with the set exposure Biolmaging Systems User Manual 5 7 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap 5 Check Use same exposure for all images in series if you want to set a single exposure for all images Note If you check both Use same exposure for all images in series and Add contents of previous images to each new image the exposure time for the first image will be the set exposure for the second image the effective exposure time will be 2x the set exposure for the third it will be 3x the set exposure and so on Uncheck Use same exposure for all images in series if you want to set a separate exposure for each of the images 6 If you have checked Use same exposure for all images in series you can adjust the exposure time as follows a Click in the exposure time control to select the hours minutes seconds or milliseconds section of the box Oimtiis 000ms b Type the new value over the numbers or click on the up or down spin arrow at the left hand end of the control to increase or decrease the number 01mElls 000ms Note You can also increase or decrease the exposure time by pressing the up or down arrow keys on the keyboard or if you are using a wheel mouse by turning the wheel c If required select another section hours minutes seconds or milliseconds and edit that number you can cli
75. amera and tighten the two locking screws to hold the connector securely in place Note There should be no movement in the cable once the screws are tightened this is essential as cable movement may lead to damage to the camera 10 Fit the Darkroom s top cover in place and fix it using the screws provided you will need a flat bladed screwdriver Fitting the UV illumination Note The Epi UV illumination is fitted as standard in ChemiGenius systems and no further action on your part is required The transilluminator is packed separately When fitted in the Darkroom it slides in and out on rails attached to its sides Biolmaging Systems User Manual 1 13 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Introduction and Initial Setup To fit the transilluminator Remove the transilluminator from its packaging Open the Darkroom door push the door up to open it Take the flying mains lead coming from the inside of the Darkroom and fit it into the mains socket on the back of the transilluminator Holding the transilluminator with its controls towards you locate the rails fixed to the side of the transilluminator into the sliding rails inside the Darkroom Push the transilluminator fully into the Darkroom Make sure that the transilluminator power switch is turned on and the intensity set to maximum see the following paragraph You should read the separate documen
76. ams or place them in word processor documents but you will not be able to reopen them in GeneSnap When you use Export Image to save an image you can choose to save the image with its annotations engraved on it or just the image Alternatively you can use Export Image to save the image annotations in a separate file To export the image or annotations in the selected Image window to a new image file 1 Choose View Original or View Processed from the View menu depending on whether you want to export the Original or Processed image or the annotations on the Original or Processed image 8 6 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com File menu 2 Choose Export from the File menu to display the Export dialog box Save in Bitmaps x al exi a Image6 bmp File name Images a E Save as type BMP Compressed y Cancel F Open as read only I Engrave Annotation I Convert to 16bit Je Genvertta got Note The Convert to 8bit check box is disabled in GeneGenius MultiGenius and GeneWizard systems for non EDR images since the images are already 8 bit Similarly Convert to 16bit is always disabled in GeneGnome systems and in EDR images for the other systems since the images are already 16 bit Both check boxes are enabled for ChemiGenius systems 3 Select a folder to hold the exported image or annotations from the
77. an Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Index Moving annotations 5 41 MultiGenius Setting up 1 7 1 10 Multiplexing 5 19 5 21 8 9 8 11 N New Image 7 7 8 2 Normal 1 1 8 18 Notes 8 23 O Open drawer 6 6 Open Image 5 18 5 19 7 7 8 2 8 3 Original image 5 23 5 27 6 17 8 19 Overview ChemiGenius 1 11 GeneGenius 1 2 1 3 GeneGnome 1 16 GeneWizard 1 17 MultiGenius 1 6 Software 1 19 1 20 P Paste 5 43 8 16 Print 7 8 8 14 8 15 Print Preview 8 13 8 14 Printer Setup 8 12 Processed image 5 23 5 27 6 17 8 19 Promote Configuration 5 4 5 5 8 31 8 32 Properties 8 20 8 23 Pseudocolor palette 5 13 5 14 6 16 6 17 R Rectangle annotation 5 30 5 31 7 4 Index 6 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Index Region of Interest Defining 5 25 5 26 Deleting 5 27 Moving 5 26 5 27 Reshaping 5 26 Report Settings 8 13 Report Titles 8 28 Reshaping annotations 5 42 Resolution 6 11 S Saturation detection 2 16 2 17 3 10 3 11 4 13 4 14 Saturation highlighting 5 13 5 14 6 16 6 17 Save Configuration As 5 2 5 3 8 29 8 30 Save Image 7 7 8 4 Save Image As 5 17 5 18 8 5 8 6 Saving annotations 5 44 5 46 8 6 8 8 Scrolling Image windows 6 13 6 15 Security Code A 2 Selecting annotations 5 41 7 4 Selector tool 7 4 Send to GeneTools 2 13 3 8 4 10 4
78. and end of the control to move the selection to the next section g 01m 40s Mims IN Note Only certain values of exposure time are allowed if you type a non allowed value directly into the box it will be corrected to the next allowed value G 2 Press the Image capture button in the Image Capture toolbox to capture the image The captured image will be shown in an Image window and the drawer will be unlatched automatically 3 4 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Capturing an image from the camera Capturing a series of images To capture a series of images E 1 Press the Image series button in the Image Capture toolbox to display the Series Capture dialog box Number of images in series 5 lt IV Add contents of previous images to each new image IV Use same exposure for all images in series Exposure control Exposure time E 01m 00s 000ms ll 2 Set the number of images in the series by clicking on the arrow buttons next to the Number of images in series spin box you can choose from 1 to 100 inclusive 3 Check Add contents of previous images to each new image if you want the results to be cumulative each new image is the result of adding the new exposure to the previous image in the series Uncheck Add contents of previous images to each new image if you want all images in the
79. and will have been fitted in the Darkroom before delivery together with any additional filters you have purchased Fitting the camera and control box For ChemiGenius systems the Darkroom is supplied with the top cover removed and the camera lens assembly and control box unmounted so you will need to fit them to the Darkroom The camera is supplied with zoom lens and close up lens already fitted Note The camera lens assembly is a sensitive instrument and must be handled with care at all times In particular you should take care to avoid touching the lens surface Note Each camera is factory configured to give optimum results with its specific lens and control box It is vital that you do not make any adjustments to this configuration in particular you must not detach the lens from the camera before fitting To fit the camera lens assembly and control box in the Darkroom 1 At the back of the Darkroom remove the camera control box compartment cover from the Darkroom this panel is at the left hand end of the Darkroom when viewed from the back and has a rectangular hole with cable slots at the top and bottom You will need a cross head screwdriver to undo the seven screws fixing the panel to the Darkroom 2 Make sure that the power button on the front of the camera control box is turned on 3 Arrange the flying power lead coming from the inside of the control box compartment so that it lies along the bo
80. anteed 888 88 SOURCE www artisantg com Hints To display the Histogram window dhi Choose Histogram from the View menu to view the Histogram window 65535 Provided the distribution lies within the range of the histogram without saturating at either end you will be able to carry out a quantitative image analysis with confidence You can also use the Histogram window to adjust the display conditions in the Image window see page 5 14 and highlight saturated areas of the image using a button on the Image window s image control bar see page 5 13 Moving on GeneSnap provides many other powerful features to help you work with captured images for details see Using GeneSnap Chapter 5 and the other reference chapters following it Biolmaging Systems User Manual 3 11 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneGnome 3 12 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneWizard This chapter gives a quick introduction to using your GeneWizard system taking you through the processes of starting up capturing an image and opening the image in GeneTools for analysis The final section of the chapter gives some hints on using GeneWizard There are other ways to carry out the operations described in this chapte
81. apture from the Extras menu When the command is checked in the menu new windows will be created in autoscale mode If you adjust the size of an Image window in autoscale mode the magnification of the image will be changed to fit the new window size You can switch an autoscaling window to fixed magnification mode using the zoom commands from the View menu or the zoom buttons You can switch a fixed magnification mode window to autoscaling mode by pressing the Zoom to Fit button 8 32 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Image Image Sharpen Sharpen Smooth Invert Flip Horizontal Flip Vertical Emboss Define Region of interest Crop to region To sharpen the image make the boundaries between areas sharper in the selected image window Choose Sharpen from the Image menu If the Image window was in View Original mode when you chose the command a copy of the Original image will be sharpened This Processed image will then replace any existing Processed image and the Image window will switch to View Processed mode If you switch back to View Original mode the original unsharpened image will be displayed If the Image window was in View Processed mode the Processed image will be sharpened If required you can sharpen a Processed image repeatedly When you sharpen an image there is a loss of
82. aptured image If you are using auto exposure the iris should be set so that there are no fully saturated areas in the image when the exposure is set to the minimum time Using EDR Extended Dynamic Range not GeneGnome GeneSnap s patented Extended Dynamic Range EDR feature allows you to extend the dynamic range of the system s camera In particular it increases the detail in low intensity areas of the image allowing you and analysis software like GeneTools to distinguish features in dark parts of the object that would otherwise be undetectable without saturating the lighter areas When you carry out an EDR exposure GeneSnap grabs a series of four images at increasing doubling exposure times GeneSnap then combines the results to form a 16 bit EDR image An important feature to note is that the exposures are combined linearly to ensure the validity of quantitative measurements taken from the EDR image When GeneSnap carries out an EDR capture it first performs an exposure at the set exposure time Provided there are no saturated maximally white areas in the image GeneSnap will then capture three more images doubling the exposure time for each The results of the four captures will then be combined into a single 16 bit image which 5 10 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using the UV light with the Darkroom s door open
83. aranteed 888 88 SOURCE www artisantg com Capturing images from the camera Capturing images using Series Capture To capture a series of one or more images with the same or individually set exposures 1 Choose the required Configuration from the Configuration toolbar s drop down list box This sets the filter lighting resolution for ChemiGenius EDR setting and Exposure time to the values saved in the Configuration However you can change these settings individually for each series of exposures if required Note If EDR is checked an EDR exposure will be carried out for each image in the series see Using Extended Dynamic Range EDR page 5 10 for details Bo 2 Press the Image series button in the Image Capture toolbox to display the Series Capture dialog box Number of images in series 5 lt IV Add contents of previous images to each new image IV Use same exposure for all images in series Exposure control Exposure time E 01m 00s 000ms ll Cancel 3 Set the number of images in the series by clicking on the arrow buttons next to the Number of images in series spin box you can choose from 1 to 100 inclusive 4 Check Add contents of previous images to each new image if you want the results to be cumulative each new image is the result of adding the new exposure to the previous image in the series Uncheck Add contents of previous images to each new image if you want
84. as a secure image file sgd 1 Choose Save Image As from the File menu to display a standard Windows Save As dialog box Save in 4 Images es exi 28 Image6 sad File name Image7 s9d CS ES j Save as type GeneSnap sgd y Cancel Len 2 Select a folder to hold the image file from the Save in drop down list and the file list box below it 3 Enter a name for the image file in the File name box 4 Press Save to save the image with the new name Note If you have processed the image in any way see Manipulating images on page 5 21 for details both the Processed and Original images will be saved together with any annotations you have placed on them see Placing annotations on an image on page 5 27 for details If you reopen the image in GeneSnap you will be able to use View Original or View Processed in the View menu to choose which version to view and the annotations will still exist as separate objects that can be moved or edited as required Biolmaging Systems User Manual 5 17 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap If the image has not been saved before an alternative to Step 1 above is 1 Choose Save Image from the File menu The remaining steps are then the same However if the image has been saved before Save Image will save the image in the existing file and will not prompt you to enter a new file name Loading image files
85. as if it were a single exposure Note Image files created using the Create new composite image command do not satisfy the conditions required for Good Laboratory Practice this fact is noted in the composite image s Capture properties see Properties page 8 20 for how to view image properties To create a new composite image from two or three other images 1 Capture or open the images you want to superimpose Note Take care not to move the gel between captures Biolmaging Systems User Manual 8 9 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Menus 2 Choose Create new composite image from the File menu to display the Create NON GLP Composite Image dialog box Create NON GLP Composite Image None leave blank None leave blank None leave blank The three color drop down list boxes at the top of the dialog box each list the currently open images together with the None leave blank item 3 Select the two or three images you want to superimpose from the color drop down list boxes When you select the first image it will be displayed in the dialog box in the list box color When you select the second and third image it will be superimposed on the first image s in its list box color 4 If you want to add one or more of the images as a negative inverting light and dark in the image check the co
86. at 0 though it is at such a low level that it may not be important information The following sections give examples of how the histogram can be used to analyze various image conditions and suggestions for how to improve the capture settings Biolmaging Systems User Manual 6 19 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The GeneSnap Application Window Note The histogram does not update while you are viewing a live image it will be updated when you capture the image Image too dark 255 65535 You should open the iris or increase the exposure time Image too light 255 66535 You should close the iris or decrease the exposure time Note The adjustments to the iris and exposure time described above are made before you recapture the image and affect the amount of information that is captured You can also use the Histogram to control the way the information is displayed but this has no effect on the amount of information captured see the following section 6 20 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The Histogram window Histogram window cursors The Histogram window shows the distribution of intensities present in the image in the selected Image window It also shows the range of the image display usi
87. bar is displayed 8 26 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Extras The annotation toolbars contain tools for adding and formatting annotations to an image See the Toolbars chapter Chapter 7 for general information about using toolbars and for a description of each of the buttons they contain Extras User name Report Titles Initial Acquire State Save Configuration As Delete Configuration Promote Configuration v Autoscale on capture User name To select a different user name enter a new one and or choose whether to display the GeneSnap User name dialog box when GeneSnap starts 1 Choose User name from the Extras menu to display the GeneSnap User name dialog box GeneSnap User name Eg User Name y F Show this dialog at program start Remove User coca 2 Select the required user name from the Name drop down list box or type in a new name 3 Check or uncheck the check box to specify whether you want this dialog box displayed each time you start GeneSnap Biolmaging Systems User Manual 8 27 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Menus Report Titles To enter data to appear at the beginning of full GeneSnap reports see Report Settings in the File menu page 8 13 for how to choose whether to print fu
88. below it 4 Enter a name for the exported image or annotations file in the File name box 5 For 8 bit images non EDR GeneGenius MultiGenius and GeneWizard or 12 bit image non EDR ChemiGenius check Convert to 16bit if you want the image saved as a 16 bit image The image will be exported as a 16 bit tiff file 6 For 16 bit images GeneGnome and EDR images check Convert to 8bit if you want the image saved as an 8 bit image 7 Select the format for saving the file from the Save as type box you can save images in a wide variety of image formats or just save the annotations in a ann file you will be able to add the saved annotations to images in GeneSnap at a later time using Merge Annotation Biolmaging Systems User Manual 5 45 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap 8 For an image export check Engrave Annotation if you want to export the image with any annotations leave it unchecked if you want to export the image only Note If you choose to export the image with annotations the annotations will become part of the exported image engraved and the underlying parts of the original image will be permanently obscured in the exported image 9 Press Save to save the image or annotations with the new name To add the annotations saved in an annotation file to the annotations if any already on the image in the selected Image window 1
89. button only appears on the Image toolbar for MultiGenius systems Sharpen Pressing the Sharpen button is equivalent to choosing Sharpen from the Image menu see page 8 33 to make the boundaries between regions in the image sharper Smooth my Pressing the Smooth button is equivalent to choosing Smooth from the Image menu see page 8 34 to make the boundaries between regions in the image smoother Speckle Correction MultiGenius only Press the Speckle Correction button to process an image by removing speckles If the Image window was in View Original mode when you chose the command a copy of the Original image will be speckle corrected This Processed image will then replace any existing Processed image and the Image window will switch to View Processed mode If you switch back to View Original mode the Original image will be displayed If the Image window was in View Processed mode the Processed image will be speckle corrected When you speckle correct an image there may be a loss of image information 7 2 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Image Invert Speckle correction is intended to remove the effects of rogue defective cells in CCD cameras being used for low light integration During speckle correction each pixel value is compared with the average of the eight adjacent pixels If it is larger than the aver
90. cal and or horizontal scroll bar You can scroll the window in the usual ways by dragging the scroll button clicking in the scroll bar either side of the scroll button or by clicking the arrow buttons at the ends of the scroll bar However you can also scroll the window by dragging as follows 1 Move the pointer over the image 2 Press the right hand mouse button the pointer will change to show that you can drag the image A v 6 14 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Image windows Also unless the image is live an overview pane will be displayed on the image showing the whole image and an outline showing the part displayed in the image 3 Either drag the image in the main pane or drag the outline in the overview pane dragging the outline scrolls the image faster The overview pane will disappear a few seconds after you stop scrolling Biolmaging Systems User Manual 6 15 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The GeneSnap Application Window Image controls The image controls at the right hand edge of Image windows control the display of the image in the window The following pictures show the function of each of the controls Grayscale Color Wash Pseudocolor Switch to pseudocolor Switch to grayscale l i Color washes E Pseudocol
91. ck on the scroll bars at the right hand end of the control to move the selection to the next section E Dim 40s ums Note Only certain values of exposure time are allowed if you type a non allowed value directly into the box it will be corrected to the next allowed value The values allowed depend on the system you are using 5 8 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Capturing images from the camera If you have unchecked Use same exposure for all images in series an additional Image number spin box is displayed in the Series Capture dialog box Number of images in series 5 IV Add contents of previous images to each new image Image number 1 of 5 4 m Exposure control Exposure time E 01m 00s 000ms ll Cancel To set the exposure for each image a Click on the up or down arrows next to the Image number spin box to choose an image number b Follow the procedure above for setting the exposure time Note If you have checked Add contents of previous images to each new image the exposure time for the first image will be the exposure set for the first image for the second image the effective exposure time will be the exposure time set for the first image plus the exposure time set for the second image for the third image it will be the sum of the exposure times set for the first
92. click on the scroll bars at the right hand end of the control to move the selection to the next section g 0im 40s Mims Note Only certain values of exposure time are allowed if you type a non allowed value directly into the box it will be corrected to the next allowed value 3 6 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Capturing an image from the camera If you have unchecked Use same exposure for all images in series an additional Image number spin box is displayed in the Series Capture dialog box Number of images in series 5 IV Add contents of previous images to each new image Image number 1 of 5 4 m Exposure control Exposure time E 01m 00s 000ms ll Cancel To set the exposure for each image a Click on the up or down arrows next to the Image number spin box to choose an image number b Follow the procedure above for setting the exposure time Note If you have checked Add contents of previous images to each new image the exposure time for the first image will be the exposure set for the first image for the second image the effective exposure time will be the exposure time set for the first image plus the exposure time set for the second image for the third image it will be the sum of the exposure times set for the first three images and so on 6 Press OK to confirm
93. conds to prevent the door being opened accidentally For GeneGnome and GeneWizard it shows whether the drawer is unlatched latched or locked the drawer is locked during exposures Freeze Go live not GeneGnome The Freeze Go live button is e Green when no Image window is showing a live image e Red when the selected Image window is showing a live image e Grey when an unselected Image window is showing a live image Note In the first two cases the button turns blue when the pointer is over it To display a live image for lens adjustment and sample positioning Gi Press the Freeze Go live button in the Image Capture toolbox Note You can only display a live image if the exposure time is set to less than 5 seconds If there is an open Image window that is currently connected to the camera and selected it will be made live otherwise a new Image window will be opened showing a live image Biolmaging Systems User Manual 6 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The GeneSnap Application Window Note If an Image window showing a live image is frozen it remains connected to the camera unless the image is processed in any way see Original and Processed View modes page 6 17 or another Image window is opened to show a Live image Once an Image window has been disconnected from the camera it cannot be reconnected The red lamp at the
94. d C Images C GrabberSupport 1 Intenet Explorer a Microsoft Hardware E Microsoft Office Y Microsoft Script Control demo63 demo63sg SS demo63h demos3h sgd SS democt democtsod democ4 Jdemoc4sod BE EL 4 E Note The picture shows the Browser in a free floating window it can also be maximized in the GeneSnap document area see page 6 22 for more details of how to work with the Browser Biolmaging Systems User Manual 8 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Menus 2 Use the left hand pane in the Browser in exactly the same way as you use the left hand pane in Windows Explorer to select the folder containing the required image The right hand pane in the Browser will show a preview of all the images in the selected folder 3 Double click on the image that you want to open Save Image Note The Save Image command is disabled when the selected Image window is showing a live image from the camera To save the grabbed image in the selected Image window to an image file Choose Save Image from the File menu If the Image has been saved previously to an image file the image will be saved again with that name Otherwise the command will behave as if you had selected Save Image As see the next section If you have processed the image in a
95. d value The values allowed depend on the system you are using 2 10 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Capturing an image If you have unchecked Use same exposure for all images in series an additional Image number spin box is displayed in the Series Capture dialog box Number of images in series 5 IV Add contents of previous images to each new image Image number 1 of 5 4 m Exposure control Exposure time E 01m 00s 000ms ll Cancel To set the exposure for each image a Click on the up or down arrows next to the Image number spin box to choose an image number b Follow the procedure given in Step 7 for setting the exposure time Note If you have checked Add contents of previous images to each new image the exposure time for the first image will be the exposure set for the first image for the second image the effective exposure time will be the exposure time set for the first image plus the exposure time set for the second image for the third image it will be the sum of the exposure times set for the first three images and so on 9 Press OK to confirm your selections close the dialog box and start the image capture Note When an exposure time greater than 30 seconds is used to capture an image the Darkroom door is automatically locked electronically during the ex
96. e You can change the capture settings while you are using a system default Configuration but if you then try to save the Configuration you will have to enter a new name and it will be saved as a new user Configuration Capturing images from the camera i You use the Image Capture toolbox to capture images To display the Image Capture toolbox if it is not displayed Press the camera button in the Standard toolbar See the chapters in the Getting Started part of this manual for more information about how to prepare the system for image capture You can capture e a single image from live video not GeneGnome e a series of one or more images with identical or individually set exposures e a single image using Auto Exposure not GeneGnome Note You are recommended not to use Auto Exposure in ChemiGenius when a Chemiluminescence Configuration is selected These processes are described in the following subsections You can use the Extended Dynamic Range EDR feature with the first two of these procedures see Using Extended Dynamic Range EDR page 5 10 for details Capturing an image from live video not GeneGnome Note You can only capture an image from live video if the exposure time is set to less than 5 seconds Biolmaging Systems User Manual 5 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap To capture a single
97. e Tiles sh ee a ee wa OR we a we oD oe 5 18 Creating a composite image multiplexing 2 o ee 5 19 Manipulating images lt s s sos s oe aoe so mkn aE anai e i ae a a IE 5 21 lIimag toolbat e ak Ss apa a a Ar aa a Me Bee oe ook 5 22 Original and Processed images 6 44 6 2a a a 5 23 Sharpening and smoothing images 2 2 a a a ee 5 23 Applying speckle correction MultiGenius only 2 o e 5 24 Inverting Images s e oe acr SG g i EEO Ga OED a BES 5 24 Embossing an image 2 a 5 25 Flipping an image s s uo dw ake a 5 25 Cropping an IMage s e c e he we pa aa Mo a ee oe a 5 25 Biolmaging Systems User Manual Contents 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Contents Placing annotations on an image s soa eos e e 5 27 Annotate toolbar o a a a a a a a a 5 27 Showing and hiding annotations o a a a a a 5 28 Selecting the default color and line style for annotations o ooo 5 28 Drawing a finess e e nicam A SHE EHS wee x 5 28 Drawing a rectangles 25 e e e p a k a n Gua a DH Gnd 5 30 Drawing an ellipse a ea a e aia o a a d a e a 5 31 Drawing a freehand Shape e c e oos ca saaa a a eoe ee 5 32 Placing texton AN image e ou alk Wa ga ORS e GR ue da a 5 37 Drawingean AOW s soa as a Re a A Se ee A ee A be a 5 39 Changing annotations s sia oe e 5 41 Exporting images and engraving saving and merging annotations
98. e display conditions in the Image window see page 5 14 and highlight saturated areas of the image using a button on the Image window s image control bar see page 5 13 Moving on GeneSnap provides many other powerful features to help you work with captured images for details see Using GeneSnap Chapter 5 and the other reference chapters following it 4 14 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Part 3 Reference Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap This first chapter in the Reference part of the manual extends the Getting Started chapters with instructions for using GeneSnap to carry out a variety of common operations Working with Configurations GeneSnap allows you to create and save Configurations containing default settings You can then change quickly from one type of work to another by selecting the appropriate Configuration to set the required filter lighting resolution for ChemiGenius EDR not GeneGnome and exposure time at the same time However if required you can change these settings individually for each exposure User and system default Configurations GeneSnap is supplied with a number of system default
99. e toolbox for ChemiGenius showing a live image some controls are hidden when the image is frozen and the sensitivity resolution drop down list box is always hidden for GeneGenius and MultiGenius systems Note Depending on what options are selected see page 8 21 an Image window may be opened automatically Capturing an image This section shows you how to carry out some typical procedures for capturing images You will learn how to e Capture an image using an automatic exposure see page 2 5 e Capture an image from live video see page 2 6 e Capture a series of images see page 2 8 e Capture an image with Extended Dynamic Range see page 2 12 Once you have understood these examples you will be able to choose and if necessary modify the technique that best suits your own requirements and the samples you are using Whichever technique you use the first task is to frame and focus the image Since this procedure is common to all the capture techniques it is described before the separate procedures Framing and focusing the image To frame and focus the image 1 Prepare the gel Note When working with chemiluminescence samples membranes may be with or without cling wrap film but note that reflections from the film can give problems However we recommend that instead you place the sample between two pieces of acetate sheet for example overhead transparency film 2 Ifa live image is currently
100. e you set the white light pad in position see Step 5 in Framing and focusing the image see page 2 3 2 Ifa live image is not currently displayed press the green Freeze Go live button in the Image Capture toolbox to display a live image in an Image window and show the lens control buttons 3 Select Lower white from the lighting control drop down list box Note If you create a Configuration for white light captures you will be able to select the illumination and other settings automatically by selecting that Configuration 4 If your system is fitted with a motorized filter wheel this is standard for MultiGenius and ChemiGenius systems but optional for GeneGenius select the EtBrUV filter or other suitable filter for the stain you are using Eev 5 Adjust the iris setting to give a good image of the gel without saturating losing detail in the dark or bright areas see Step 8 in Framing and focusing the image see page 2 3 for how to set the iris see Adjusting display conditions page 5 13 for how to tell when an image is saturating 6 Press the red Freeze Go live button in the Image Capture toolbox The image will be captured frozen in the Image window ready for further processing annotation or analysis as required The light inside the Darkroom will be switched off automatically after the final exposure to minimize any damage to the sample Biolmaging Systems User Manual 2 7 Artisan Techno
101. ecific points you should note There are three controls on its front from left to right these are a knob controlling the UV intensity a switch to bypass the intensity control and a master on off switch When you switch on the UV light or when it is switched on automatically by GeneSnap the intensity should be set to maximum to ensure that the lamps strike You can set the intensity to maximum by turning the intensity knob fully clockwise or by disabling it using the bypass switch Fitting the white light pad Note The Epi white light illumination is fitted as standard and no further action on your part is required To fit the white light pad 1 Remove the white light pad from its packaging 2 Open the Darkroom door push the door up to open it 3 Hold the white light pad with the front towards you and place it on the transilluminator in the Darkroom when placed correctly the white light pad s power supply socket is on the left hand side and towards the back 4 Take the flying low voltage power supply lead coming from the inside of the Darkroom and fit it into the white light pad s power supply socket 5 Make sure the power button on the side of the white light pad is turned on 1 4 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com GeneGenius This is how the white light pad should be located when you are using it If you wan
102. ed image and the Image window will switch to View Processed mode If you switch back to View Original mode the original unflipped image will be displayed If the Image window was in View Processed mode the Processed image will be flipped When you flip an image there is no loss of image information GeneSnap allows you to produce a 3 D embossed view of the image emphasizing the boundaries between regions Biolmaging Systems User Manual 8 35 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Menus To emboss the image Choose Emboss from the Image menu If the Image window was in View Original mode when you chose the command a copy of the Original image will be embossed This Processed image will then replace any existing Processed image and the Image window will switch to View Processed mode If you switch back to View Original mode the original unembossed image will be displayed If the Image window was in View Processed mode the Processed image will be embossed When you emboss an image there is a loss of image information Define Region of Interest In order to crop an image you need to define the region of interest first To define an area to crop to 1 Choose Define Region of Interest from the Image menu When you move the pointer over the image it changes to a cross hair 8 36 Biolmaging Systems User Manual Artisan Technology Group
103. ed in the Tools menu when the Image toolbar is displayed Biolmaging Systems User Manual 8 25 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Menus Displaying the Image toolbar automatically hides the annotation toolbars See the Toolbars chapter Chapter 7 for general information about using toolbars and for a description of each of the buttons they contain Annotate To display or hide the annotation toolbars Annotate Color and Line Style E Choose Annotate from the Tools menu Annotate is checked in the Tools menu when the annotation toolbars are displayed Displaying the annotation toolbars automatically hides the Image toolbar The annotation toolbars contain tools for adding and formatting annotations to an image See the Toolbars chapter Chapter 7 for general information about using toolbars and for a description of each of the buttons they contain Zoom To display or hide the Zoom toolbar Choose Zoom from the Tools menu Zoom is checked in the Tools menu when the Zoom toolbar is displayed The Zoom toolbar contains tools for changing the magnification of the image See the Toolbars chapter Chapter 7 for general information about using toolbars and for a description of each of the buttons they contain Standard To display or hide the Standard toolbar Choose Standard from the Tools menu Standard is checked in the Tools menu when the Standard tool
104. eehand shape Note You can select the Select tool when the Draw Freehand Shape tool is selected by pressing the Select button on the Annotate toolbar 5 36 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Placing annotations on an image Placing text on an image To place a text annotation on an image A 1 Press the Draw Text button After you have pressed the button the pointer changes shape when it is over the image If you want to change the text orientation and or font from the current defaults double click on the image to display the Caption dialog box otherwise go straight to Step 3 ua Fi t Orientation foto fe Horizontal Vertical a Click on a radio button to choose whether the text should be Horizontal or Vertical with the text rotated by 90 Biolmaging Systems User Manual 5 37 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap b Press Font to display the Font dialog box Font Font Font style Bial Bold Arial Black Tr Arial Monospaced T Arial Narrow Tr Arial Narrow Special G Tr Arial Narrow Special G T Arial Rounded MT Bol Sample AaBbYyZz Script Westem y This is a standard Windows Font dialog box c d 8 h Choose the required typeface from the
105. eneSnap GeneSnap starts automatically when you turn on the PC However if you close it for any reason you can restart it without having to restart the PC by double clicking on the GeneSnap icon on the Windows Desktop Xd t s 2588 GeneSnap from SynGene Logging in If you do not want to display the log in dialog box automatically when the program starts uncheck the Show this dialog at program start box GeneSnap User name Eg User Name A N Other Ex T Show this dialog at program start Remove User Cancel _ The last user will be logged in automatically when the program starts You can use User name in the Extras menu to log in a different user and or choose to display the log in dialog box on program start up again Displaying the Image Capture toolbox To display the Image Capture toolbox if it is not displayed Press the camera button in the Standard toolbar 2 14 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Hints Image exposure You can control the brightness of the image by changing the exposure time as well as by opening or closing the iris To change the exposure time a Click in the exposure time control in the Image Capture toolbox to select the hours minutes seconds or milliseconds section of the box 00m Hs 000ms b Type the new value over the numbers or click on the up or down spin
106. enu when annotations are shown Selecting the default color and line style for annotations You can choose the default color and line styles to be used for new annotations by pressing buttons in the Color toolbar MODAN AO and Line Style toolbar Note It is often better to use black or white annotations if you are going to print on a black and white printer since coloured annotations may not stand out clearly You can also change the color and line style used for existing annotations by selecting them and pressing the appropriate buttons in the toolbar see page 5 41 for how to select annotations There are no menu equivalents for the operations carried out using the Color and Line Style toolbars Drawing a line N To draw a line annotation on an image 1 Press the Draw Line button 5 28 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Placing annotations on an image 2 Move the pointer to the position where you want to place one end of the line When the Draw Line tool is selected the pointer changes to a cross hair when it is over the image 3 Press and hold down the mouse button then drag to the position where you want to place the other end of the line 4 Release the mouse button to place the line on the image When you have placed the line on the image the Draw Line tool
107. ept speckle correction Original and Processed images GeneSnap protects your original images by applying manipulations to a copy of the Original image the Processed image You can then apply further manipulations to this Processed image You can choose whether to display the Original or the Processed image in an Image window To display the Original or Processed image in the active image window Choose View Original or View Processed from the View menu View Processed is disabled if there is no Processed image When the Processed image is displayed the name of the image shown in the Image window s title bar is followed by a hyphen and a number showing the number of processing actions that have been performed on the image Note If you choose one of the image manipulation commands when an Original image is displayed the change will be applied to a new Processed image the new change will replace any existing ones However if a Processed image is displayed the change will be applied to the existing Processed image the new change will be added to any existing ones When you save an image using Save Image or Save Image As the resulting file will contain both the Original and Processed images If you want to save the Processed image only in a standard graphics format file display the Processed image in the Image window and choose Export Image from the File menu see page 8 6 Sharpening and smoothing images
108. eration that changes the image values e if the Image window is in View Processed mode the Processed image will be processed further e if the Image window is in View Original mode a copy of the Original image will be processed Biolmaging Systems User Manual 6 17 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The GeneSnap Application Window In both cases the new Processed image will replace any existing one When you choose Save or Save As from the File menu to save an image both the Original image and the Processed image will be saved in a single file if you reopen the image you will be able to display either the Original or Processed image in the usual way If you want to save the Processed image only in a standard graphics format file display the Processed image in the Image window and choose Export Image from the File menu see page 8 6 The Histogram window Showing and hiding the Histogram window dki To show or hide the Histogram window Choose Histogram from the View menu Note When the Histogram window is floating see next section you can also hide the Histogram window by clicking on the close button at its top right hand corner Docking and floating the Histogram window By default the Histogram window is docked below the Image Capture toolbox on the left hand side of the GeneSnap Application Window However you can make it float
109. esponse program You can determine the Media Key in use on existing systems from the About dialog box in GeneTools choose About from the Help menu Note that some versions of GeneTools may reformat the Media Key by changing any asterisks into dashes You should use the format shown on the insert card or case that came with the GeneTools CD The insert card also has space for you to record which system was used for each Media Key Installing boards This section describes the procedure for installing the framegrabber GeneGenius or MultiGenius or Firewire ChemiGenius board the same procedure is used for both types of board Note Electronic components can be damaged by electrostatic charge that has accumulated on your body discharging through them This damage is not always immediately apparent and can cause unpredictable errors or premature failure To prevent this happening avoid wearing clothing made from materials that can generate large electrostatic charges such as wool or some artificial fibers Use an electrostatic discharge protection kit if you have one or use the anti static bag in which the board is supplied as a temporary antistatic mat Before picking up the board from the mat place one hand on the mat and use the other hand to pick up the board Handle the board using the metal end plate and avoid touching any connectors or other conducting components When inserting the board in the PC hold the PC chassis
110. ety of information see the next section for details Image windows Image windows are standard Windows document windows which you can minimize restore move and resize in the normal way You can use commands in the Window menu to tile the non minimized Image windows and Browser if it is not minimized cascade them and if they are minimized arrange their icons See page 6 12 for more information about using Image windows Image Capture toolbox By default the Image Capture toolbox is docked to the left hand side of the GeneSnap Application Window However you can make it float freely on the desktop or dock it to another edge of the window The Image Capture toolbox is not affected by the tiling or cascading commands and if it overlaps an Image window it is always displayed on top Histogram window The Histogram window can be shown hidden moved and resized but not minimized The Histogram window is not affected by the tiling or cascading commands and if it overlaps an Image window it is always displayed on top See page 6 18 for more information about using the Histogram window Browser The Browser allows you to preview and open saved image files If it is non minimized the Browser will be tiled and cascaded with the non minimized Image windows by the tiling and cascading commands See page 6 22 for more information about using the Browser Biolmaging Systems User Manual 6 1 Artisan Technology Group Quality Instrumentation
111. f you save the image you cannot undo a change that was made before saving the image Note Some changes for example moving an annotation do not cause a copy to be saved Choosing Undo reverts the image to its state before the last major change so any minor changes made since then will also be undone View Y Annotation v Histogram v Grid on Live Normal 1 1 Zoom In Zoom Out View Original v View Processed Properties Alt Enter Status Bar Note The picture above shows the View menu when an Image window is selected If no windows are open the menu only contains the Histogram and Status Bar commands Annotation To view or hide any annotations on the image in the selected Image window Choose Annotation from the View menu Annotation is checked in the menu when annotations are displayed on the selected Image window Biolmaging Systems User Manual 8 17 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Menus Note Annotations are not displayed in an Image window showing live video even if Annotation is selected Histogram To view the Histogram window showing the distribution of intensities in the image in the selected Image window dhi Choose Histogram from the View menu To hide the Histogram window Click on the close button at the top right hand corner of the Histogram window See page 6 18 for more information abo
112. he image If you select the rectangle annotation using the Select tool drag handles will appear on its corners and in the middle of its sides so that you can move or reshape the rectangle Note You can select the Select tool when the Draw Rectangle tool is selected by pressing the Select button on the Annotate toolbar Drawing an ellipse To draw an ellipse or circle annotation on an image 1 Choose whether to draw a filled or hollow ellipse press the Hollow Filled Shape button if the Draw Ellipse button shows the wrong sort of ellipse or Press the Draw Filled Ellipse button C 2 Press the Draw Hollow Ellipse button You will draw the ellipse by dragging out the bounding rectangle for it on the image 3 Move the pointer to the position where you want to place one corner of the ellipse s bounding rectangle When the Draw Ellipse tool is selected the pointer changes to a cross hair when it is over the image Biolmaging Systems User Manual 5 31 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap 4 Press and hold down the mouse button then drag the pointer to the opposite corner of the ellipse s bounding rectangle When you have placed the ellipse on the image the Draw Ellipse tool will still be selected so that you can place other ellipses on the image If you select the ellipse annotation using the Select tool drag handles will appea
113. he image display will be fully black or fully white in other words the display will have low contrast To adjust the image display using the cursors in the Histogram window 1 Move the pointer over the cursor you want to adjust The pointer will change to a two headed arrow showing that you can drag the cursor i Histogram x e The example shows the Histogram window with an 8 bit image you use exactly the same procedure for a 16 bit image 2 Press the mouse button and drag the cursor to its new position Histogram x 3 Release the mouse button to drop the cursor in its new position To reset the cursor lines to the minimum and maximum values Double click in the Histogram window Note You can also use the Histogram window to judge whether the exposure of an image could be improved for example whether a large amount of information is being lost because it is saturating See The Histogram window in The GeneSnap Application Window chapter page 6 18 for details 5 16 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Saving and loading image files Saving and loading image files To save the image in the active Image window to a new image file Note See Exporting images and engraving saving and merging annotations page 5 44 for how to save the image in a format other than
114. hods above either Choose an EDR Configuration after Step 1 Gel sample EDR Check EDR in the Image Capture toolbox See Using EDR Extended Dynamic Range not GeneGnome page 5 10 for more information about EDR Note EDR is not suitable for use with chemiluminescence samples because of the long exposures required due to the low levels of light they emit Analyzing the image The next step after capturing an image is to analyze it to do this you will use SYNGENE s GeneTools To start up GeneTools to analyze the image in the selected Image window ot fas 1 Press the Send to GeneTools button 4 10 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Hints A standard Windows Save As dialog box will open so that you can save the image file Save in 4 Images es exi 28 Image6 sad File name Image sgd L y Save as type GeneSnap sad y Cancel Zi 2 Select a folder to hold the image file from the Save in drop down list and the file list box below it 3 Enter a name for the image file in the File name box 4 Press Save to save the image with the new name Once you have saved the image GeneTools will open with the image loaded ready for you to analyze it see your GeneTools documentation for how to use GeneTools Hints This section gives a few further hints to help you s
115. ientation and or font in a text annotation 1 Double click on the annotation to select it drag handles control points will appear around the text to show it is selected and display the Caption dialog box Biolmaging Systems User Manual 5 43 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap Note You can double click the text annotation with either the Selector tool or Draw Text tool m FE p Orientation fot Z Horizontal C Vertical The edit box shows the text in the selected annotation you can edit the annotation text here if required 2 Use the Caption dialog box to change the text orientation and or font as required see page 5 37 for further details of how to use the Caption dialog box Exporting images and engraving saving and merging annotations The annotations you place on an image exist as separate objects from the image This means that adding an annotation leaves the image data unchanged and it means that you can move edit or delete the annotations independently of the image When you save an image using Save Image or Save Image As any annotations on the Original and if it exists Processed images are also saved in the image file but as separate objects so you can still move edit or delete the annotations when you reopen it See Saving and loading image files page 5 17 for details This section shows you h
116. il For presentation purposes you can process captured images to create a negative image and increase or decrease the sharpness and in MultiGenius systems apply speckle star field correction You can also crop images or flip them horizontally or vertically GeneSnap also allows you to add graphical and textual annotations You can save the annotations in a separate file from the image to transfer them to other images All processing is performed on a copy of the original image which is saved with the original image In accordance with Good Laboratory Practice GeneTools always analyses the original unprocessed image in the image file Biolmaging Systems User Manual 1 19 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Introduction and Initial Setup Original and Processed images can be exported to files using a wide range of standard graphics formats and you can choose whether or not to engrave the annotations on the exported image GeneTools GeneTools is an extremely powerful and easy to use gel analysis program It is fully automated allowing analyses to be carried out in seconds However it is also extremely flexible giving you the option to control every aspect of the analysis manually if you wish See the separate GeneTools documentation for details Summary Your Biolmaging system should now be fully assembled and ready for use You should now go to the app
117. ill be the set exposure for the second image the effective exposure time will be 2x the set exposure for the third it will be 3x the set exposure and so on Uncheck Use same exposure for all images in series if you want to set a separate exposure for each of the images Biolmaging Systems User Manual 2 9 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneGenius MultiGenius or ChemiGenius 8 If you have checked Use same exposure for all images in series you can adjust the exposure time as follows a Click in the exposure time control to select the hours minutes seconds or milliseconds section of the box 01m iis 000ms b Type the new value over the numbers or click on the up or down spin arrow at the left hand end of the control to increase or decrease the number 01mElls 000ms Note You can also increase or decrease the exposure time by pressing the up or down arrow keys on the keyboard or if you are using a wheel mouse by turning the wheel c If required select another section hours minutes seconds or milliseconds and edit that number you can click on the scroll bars at the right hand end of the control to move the selection to the next section g 0im 40s Mims Note Only certain values of exposure time are allowed if you type a non allowed value directly into the box it will be corrected to the next allowe
118. image from live video 1 Choose the required Configuration from the Configuration toolbar s drop down list box This sets the filter lighting resolution for ChemiGenius EDR setting and exposure time to the values saved in the Configuration However you can change these settings individually for each exposure if required 2 Press the green Freeze Go live button at the top of the Image Capture toolbox The button will turn red live video will be displayed in an Image window a new Image window will be opened if necessary and the lens controls will be displayed below the Freeze Go live button in the Image Capture toolbox 3 Adjust the focus zoom iris aperture and exposure as required see the chapters in the Getting Started part of this manual for more information 4 Press the red Freeze Go live button in the Image Capture toolbox Capturing a single image GeneGnome only To capture a single image in GeneGnome 1 Choose the required Configuration from the Configuration toolbar s drop down list box This sets the exposure time to the value saved in the Configuration However you can change this setting for an individual exposure if required p 2 Press the Single exposure button The button will turn red while the image is being captured and the icon in the Image Capture toolbox will show that the drawer is locked 5 6 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Gu
119. ion so it is usually convenient to maintain this convention Note You can choose Grid on Live from the View menu to display a grid on the image to help you line up the gel 7 Press the green Freeze Go live button in the Image Capture toolbox to display a live image in the Image window and show the lens control buttons 2 4 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Capturing an image Note The exposure time should be set to a low figure less than a second to ensure the image responds rapidly to any changes you make this will be the case if you chose the Gel sample Configuration at Step 3 8 Use the iris buttons to open or close the iris until you get a reasonably bright image of the gel without saturating any part of it 9 If necessary adjust the position of the gel on the transilluminator or white light pad so that it is centered in the image 10 Use the zoom buttons to frame the gel the gel should be as large as possible provided all the relevant area is included you may need to reposition the gel slightly 11 Use the focus buttons to set the best focus on the gel Note It is better to concentrate on the wells or gel edge when focuussing since the bands are inherently fuzzy 12 Close the Darkroom s door the icon on the Image Capture toolbox in GeneSnap shows when the door is clo
120. isable the appropriate device driver To disable a device driver 1 Start the PC and log in to Windows NT4 as a user with Administrator privileges for the PC 2 Choose Control Panel from the Start gt Settings submenu to display the Control Panel 3 Double click on the Devices icon Biolmaging Systems User Manual Appendix 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Appendix PC Board and Software Installation 4 Locate the driver that you want to disable in the list and press the Startup button the driver for the framegrabber is called Prymo the driver for the Firewire board is called Synoptics CG2 1 5 Choose Disabled or Manual and press OK Appendix 6 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Index A About GeneSnap 8 39 8 40 Aligning annotations 5 42 Annotate toolbar 5 27 5 28 7 4 7 5 7 8 8 26 Annotations 5 27 5 46 Adding a text annotation 5 37 5 39 Aligning 5 42 Copying 5 43 Default color and line styles 5 28 7 6 Deleting 5 42 Drawing a freehand shape 5 32 5 36 Drawing a line 5 28 5 29 Drawing a rectangle 5 30 5 31 Drawing an arrow annotation 5 39 5 41 Drawing an ellipse 5 31 5 32 Editing text annotations 5 43 5 44 Engraving 5 44 5 46 Hollow Filled Shapes 7 5 Merging 5 44 5 46 8 8 Moving 5 41 Reshaping 5 42 Saving 5 44 5 46 8 6 8 8
121. ith GeneGnome 3 SWITCHING ON s ak a ee e Gee A ee ee 3 1 Capturing an image from the camera 2 2 e 3 3 Capturing a single IMag ss s sa 4 02 4 aoe be RO we RA 3 4 Capturing a series of images p o sace e 3 5 Analyzing the IMAB s co s o RR RR DR RR AE A 3 8 EMS 3 06 a AL E NA A ee a A 3 9 Starting GeneSnap oa A a eS 3 9 LOGGING IM co Ghee a a e a A ee a 3 9 Displaying the Image Capture toolbox o a a a a a a 3 9 Image display sace die a ee a Ee Raed a Ra ak ae Wak ee oh 3 10 Saturation detection a a a be Ga Sea PE OER ba aa ee 3 10 MOVING OM i a o rar gh we et BES Begs oe Oe Ge Aa we ee en bh Ee ie 3 11 Getting Started with GeneWizard 4 SWITCNINESON 4 ace Gus Ga ee a ok PR 4 ER eae Vw 2S wes a 4 1 Capturing an image from the camera 2 2 ee 4 3 Inserting thessampl s vs a oa Swe HOE Sg YY aE E Soe we 4 3 Capturing an image using automatic exposure 2 2 1 ee 4 4 Capturing an image from live video a 2 a a 4 5 Capturing a series of images 2 2 e eo 4 6 Capturing an image with Extended Dynamic Range 4 10 Analyzing the IMAGE s gos ao e wo a a a aaa 4 10 Contents 2 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Contents P shee ea ci A felch Ae eas Br Atte had Wasa Be Me ok ce hte dete 4 11 Starting GenmeSnapis ic p s ae wR wd aoe
122. l be inverted This Processed image will then replace any existing Processed image and the Image window will switch to View Processed mode If you switch back to View Original mode the original uninverted image will be displayed If the Image window was in View Processed mode the Processed image will be inverted When you invert an image there is no loss of image information 8 34 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Image Flip Horizontal te To flip the image horizontally swap left and right Choose Flip Horizontal from the Image menu If the Image window was in View Original mode when you chose the command a copy of the Original image will be flipped This Processed image will then replace any existing Processed image and the Image window will switch to View Processed mode If you switch back to View Original mode the original unflipped image will be displayed If the Image window was in View Processed mode the Processed image will be flipped When you flip an image there is no loss of image information Flip Vertical a Emboss To flip the image vertically swap top and bottom Choose Flip Vertical from the Image menu If the Image window was in View Original mode when you chose the command a copy of the Original image will be flipped This Processed image will then replace any existing Process
123. ll summary or image only reports see Print in the File menu page 8 14 for how to print reports 1 Choose Report Titles from the Extras menu to display the GeneSnap General Options dialog box GeneSnap General Options xi Laboratory Heading 2 Enter a name to identify your Laboratory 3 Enter any other text you want to appear in the report Heading 4 Press OK to confirm the new settings and close the dialog box Initial Acquire State To set the acquisition properties to be used when GeneSnap is started up 1 Choose Initial Acquire State from the Extras menu to display the GeneSnap Initial Acquire Settings dialog box GeneSnap Initial Acquire Settings x r Live image state C Live image if was live in previous session Take snapshot only m Document state Open new document at program start C Do not open new document Cancel 8 28 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Extras Note The Take snapshot only radio button should be left selected in the Live Image state box In the Document state box click on a radio button to choose whether a new Image window showing the camera image should be opened automatically when you start up GeneSnap Save Configuration To create a new user Configuration with the current settings or to save any changes you have made since
124. located behind the camera near the back of the compartment 4 Tighten the two locking screws to hold the D connector securely in place Note There should be no movement in the cable once the locking screws are tightened this is essential as cable movement may cause damage to the camera 5 Fit the connectors at the other end of the camera cable to the matching connectors on the back of the camera 6 Fit the D connector on the lens control lead into the matching connector in the Darkroom it is located between the camera and the camera cable connector 7 Tighten the two locking screws to hold the D connector securely in place 8 Fit the Darkroom s top cover in place and fix it using the screws provided you will need a flat bladed screwdriver Fitting the UV illumination Note If you have purchased the Epi UV illuminator option for MultiGenius it will have been fitted in the Darkroom before delivery and no further action on your part is required The transilluminator is packed separately When fitted in the Darkroom it slides in and out on rails attached to its sides To fit the transilluminator 1 Remove the transilluminator from its packaging 2 Open the Darkroom door push the door up to open it 1 8 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com MultiGenius Take the flying mains lead coming from the i
125. logy Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneGenius MultiGenius or ChemiGenius Capturing a series of images You can use this capture procedure in any of the Biolmaging systems However it is particularly useful for chemiluminescence samples which require a long exposure that can be difficult to assess in advance By taking a series of exposures of different lengths you will be able to bracket the expected exposure with longer and shorter exposure times and then choose the best image from the series The following example describes how to use series capture for a chemiluminescence sample but a very similar procedure can be used for other types of sample omit Step 2 To capture an image from a chemiluminescence sample 1 Follow the procedure in Framing and focusing the image see page 2 3 to prepare the system for capturing an image 2 Press the iris button for a couple of seconds to ensure the iris is fully open 3 Select the Chemi sample Configuration from the drop down list box in the Configuration bar at the top of the GeneSnap window this ensures that no lighting and no filter will be used Chemi sample y Note GeneGenius is not designed for use with chemiluminescence samples so is not supplied with a Chemi sample Configuration You should omit Step 3 if you are using GeneGenius or if you want to carry out a series exposure
126. lso means that this installation will only work on the PC used to generate the Request Key 10 Unless you have already received the reply from SYNGENE with your security code press Cancel to close the Install Wizard if you have received the security code from SYNGENE press next to display the Install Wizard Security Code dialog box see Step 12 Note You may wish to install the Framegrabber or Firewire board while you are waiting for the reply from SYNGENE see next section Appendix 2 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Installing boards 11 When you receive the security code from SYNGENE start up the Install Wizard again choose Install Wizard from the Start gt Programs gt SYNGENE submenu The Install Wizard Security Code dialog box will be displayed 12 Type in the Security Code EXACTLY as it appears from SYNGENE and press Next to register the Security Code and complete the installation Once you have fitted the framegrabber board connected up the system components and installed the software you are ready to run the system for the first time Note Some systems are sold with multiple copies of GeneTools Each copy will have a different but very similar Media Key usually differing by only one digit If you mistakenly re use a Media Key you will receive a rejection message from the automatic r
127. luminator e Epi UV illuminator optional e UV IR filter e Motorized filter wheel with UV filter optional other filters also available e UV protective screen e PC fitted with a framegrabber high resolution monitor keyboard and mouse e Thermal printer e GeneSnap acquisition software Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com GeneGenius e GeneTools match analysis software e Microsoft Office Small Business Edition optional If you have purchased a complete GeneGenius system from SYNGENE the framegrabber board and all necessary software will have been installed in the PC so all you need to do is connect up the various system components See the appendix at the end of this manual if you have not purchased a complete system Setting up the Darkroom GeneGenius systems are supplied with the camera lens assembly fitted in the Darkroom If you have purchased the motorized filter wheel option it will have been fitted in the Darkroom before delivery together with any additional filters you have purchased If you have not purchased this option the UV IR filter will be fitted to the lens assembly Note The motorised filter wheel and EPI UV or blue lighting can be retro fitted if required contact SYNGENE for details Fitting the top cover to the Darkroom The Darkroom is supplied with the top cover removed f
128. mode at any time To reset an Image window to autosizing mode 1 Select the window 2 Press the Zoom to Fit button The Zoom to fit button is disabled when the selected Image window is in autosizing mode You can use the commands in the View menu see page 8 18 or buttons in the Zoom toolbar see page 7 6 to adjust the magnification of the display Biolmaging Systems User Manual 6 13 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The GeneSnap Application Window You can also adjust the magnification of the display using the wheel on a wheel mouse as follows If the display is in autosizing mode choose one of the zoom commands from the View menu see page 8 18 or press one of the buttons in the Zoom toolbar see page 7 6 to switch to fixed magnification mode Move the pointer over the image to the point about which you want to adjust the magnification this point will stay in view whatever the magnification Roll the mouse wheel forwards to increase the magnification or backwards to decrease the magnification you can hold CTRL or SHIFT down as you roll the wheel to zoom in smaller steps Note For a non live image if the image is larger than the window an overview pane will be displayed as you zoom using a mouse wheel see below for how to use this pane to scroll the image If the image is larger than the window the window will have a verti
129. mportant parts of the image saturating and losing detail Note It is important to make sure that the image brightness and contrast controls are set to their default positions before adjusting the exposure time and iris settings see the note at the start of Adjusting display conditions page 5 13 for more details To check for image saturation Press the Show saturated areas button in the image control bar at the right hand edge of the image window 2 16 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Hints When saturation mode is on the Show saturated areas button is depressed To switch saturation mode off E Press the Show saturated areas button again You can also judge the degree of saturation by displaying the Histogram window To display the Histogram window dhi Choose Histogram from the View menu to view the Histogram window Provided the distribution lies within the range of the histogram without saturating at either end you will be able to carry out a quantitative image analysis with confidence You can also use the Histogram window to adjust the display conditions in the Image window see page 5 14 and highlight saturated areas of the image using a button on the Image window s image control bar see page 5 13 Moving on There are other ways to carry out the operations described in this chapter
130. n extended dynamic range 16 bits when capturing images Check E D R 16 bit When EDR is selected the automatic exposure button is disabled See page 5 10 for more information about using EDR Sensitivity resolution ChemiGenius only The ChemiGenius camera allows you to optimise the balance between resolution and sensitivity the sensitivity can be increased at the cost of resolution by binning pixels together You may want to increase the sensitivity to reduce the exposure time required for chemiluminescence samples To set the balance between resolution and sensitivity Choose the required setting from the Sensitivity resolution drop down list box You can select e High resolution no binning e Medium sensitivity 2x2 bins e High sensitivity 4x4 bins e Max sensitivity 8x8 bins Biolmaging Systems User Manual 6 11 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The GeneSnap Application Window Filter wheel control not GeneGnome or GeneWizard Note The filter wheel is supplied as standard with ChemiGenius and MultiGenius It is an option for GeneGenius the control is hidden if the filter wheel is not fitted EtBr UV y The drop down list box lists the filters installed in your system To choose which filter to use Select the required filter or No Filter from the filter drop down list box The filter drop down list box
131. nGene Data sgd y Cancel Browse If you wish you can press Browse to close the Open dialog box and display the file browser window instead see the next command Browse for how to use the file browser window Select the folder holding the image file using the Look in drop down list and the file list box below it 8 2 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Biolmaging Systems User Manual File menu 3 Select the required file by clicking on it in the file list box 4 Press Open to open the image file in a new Image window If the image had been processed in any way before it was saved both the Processed and Original images will be opened choose View Original or View Processed from the View menu to select which version to view If there were any annotations on the image when it was saved the annotations will still exist on the image as separate objects that can be moved or edited as required Browse To open an existing image file using the Browser 1 Choose Browse from the File menu to display the Browser im Browser Desktop demo62x sqd demo62 sqd El B My Computer a 3 Floppy A o Win 98 C A My Documents EI Newfonts 9 Program Files E Accessories C GeneDirectory C GeneSnap C GeneTools C Backup C Demo Chemi Images C Demo Colony Images y Demo Gel Images E Demo Spotblot Images C Getting Starte
132. nd resize if necessary the open non minimized Image and Browser windows so that they are non overlapping and one above the other Choose Tile Horizontal from the Window menu Tile Vertical To arrange and resize if necessary the open non minimized Image and Browser windows so that they are non overlapping and side by side Choose Tile Vertical from the Window menu Arrange Icons To tidy up the icons title bars representing minimized Image and Browser windows so that they are in a row along the bottom edge of the GeneSnap Application window Choose Arrange Icons from the Window menu 8 24 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Tools Close All To close all of the open Image and Browser windows Choose Close All from the Window menu If any of the Image windows contain unsaved grabbed images from the camera you will be asked if you want to save the changes Windows open in GeneSnap The Image and Browser windows currently open in GeneSnap are listed at the bottom of the Window menu To select one of the open Image or Browser windows Select it from the list in the Window menu or Click in it Tools v Image Annotate v Zoom v Standard Note The Tools menu is hidden when no Image window is open Image To display or hide the Image toolbar S Choose Image from the Tools menu Image is check
133. ness 4 a kel Reset contrast to default w Adjust contrast m bil Reset Gamma correction B Reset Gamma correction E Reset Gamma correction Adjust Gamma correction I Adjust Gamma correction T Adjust Gamma correction E Show saturated areas The Show saturated areas button at the bottom of the grayscale control allows you to display any areas in the image that have saturated on black or white in blue and red respectively this can help you optimize the gain and other settings on the camera to use the largest range without saturation Note Gamma correction allows you to adjust the midtones in an image without changing the lightest and darkest tones it determines the shape of the response curve between the black and white points which are fixed by the brightness and contrast settings Using the Histogram window to control the image display You can use the Histogram window to control the image display To view the Histogram window dhi Choose Histogram from the View menu 5 14 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Adjusting display conditions To hide the Histogram window Click on the close button at the top right hand corner of the Histogram window The Histogram window shows the distribution of intensities in the selected Image window It also shows the range of the image
134. ng the Zoom In button is equivalent to choosing Zoom In from the View menu to produce a more magnified view of the image Zoom Out a Pressing the Zoom Out button is equivalent to choosing Zoom Out from the View menu to produce a less magnified view of the image 7 6 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Standard Zoom 1 1 Q Pressing the Zoom 1 1 button is equivalent to choosing Normal 1 1 from the View menu to return to an unmagnified view of the image Zoom to Fit H Press the Zoom to Fit button to adjust the magnification of the image in the selected Image window so that it is the largest possible without any parts of it being hidden When you press the Zoom to Fit button for an Image window it stays depressed for that Image window until you press one of the other zoom buttons or select one of the zoom commands from the View menu If you adjust the size of an Image window while the Zoom to Fit button is depressed the magnification of the image will be changed to fit the new window size There is no menu command equivalent to pressing this button Standard New Save meee ABA H aah Pressing the New button is equivalent to choosing New Image from the File menu see page 8 2 to open a new Image window showing a live image from the camera Pressing the Open button is equivalent to choosing Open Image from the
135. ng two vertical red cursor lines The left hand cursor shows the image intensity that is displayed as black in the Image window and the right hand cursor shows the image intensity that is displayed as white Any parts the image with intensities to the left of the left hand cursor or to the right of the right hand cursor will be displayed as black or white respectively Note For GeneGenius MultiGenius ChemiGenius and GeneWizard when the Histogram window is displayed the status bar shows the position of the left hand Black and right hand White cursors instead of the brightness and contrast For GeneGnome the status bar always shows the position of the left hand Black and right hand White cursors even if the Histogram window is hidden In the examples above the cursor lines lie outside the actual distribution so no parts of the image display will be fully black or fully white in other words the display will have low contrast Controlling the image display You can adjust the image display by dragging the cursors in the Histogram window see Using the Histogram window to control the image display page 5 14 in the Using GeneSnap chapter for details Biolmaging Systems User Manual 6 21 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The GeneSnap Application Window Browser To display the Browser Choose Browse from the File menu
136. ns page 5 1 for more information about GeneSnap Configurations Delete Configuration To delete a user Configuration you cannot delete a system default Configuration in GeneSnap 1 If the Configuration you want to delete is not the current Configuration select it using the Configuration list in the Configuration bar see page 7 9 2 Choose Delete Configuration from the Extras menu You will be asked to confirm that you want to delete the Configuration GeneSnap Al Do you really want to delete the current configuration 3 Press Yes to delete the Configuration 8 30 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Extras Promote Configuration Note Once you have promoted a user Configuration to be a system default Configuration you will not be able to edit or delete it To promote a user Configuration to be a system default Configuration 1 If the Configuration you want to promote is not the current Configuration select it using the Configuration list in the Configuration bar see page 7 9 Note If you make any changes to the capture settings after selecting the Configuration you want to promote the changed settings not the original ones will be saved in the promoted Configuration 2 Choose Promote Configuration from the Extras menu to display the Promote to System Default Configuration dialog box P
137. nside of the Darkroom and fit it into the mains socket on the back of the transilluminator Holding the transilluminator with its controls towards you locate the rails fixed to the side of the transilluminator into the sliding rails inside the Darkroom Push the transilluminator fully into the Darkroom Make sure that the transilluminator power switch is turned on and the intensity set to maximum see the following paragraph You should read the separate documentation supplied with the transilluminator However there are a few specific points you should note There are three controls on its front from left to right these are a knob controlling the UV intensity a switch to bypass the intensity control and a master on off switch When you switch on the UV light or when it is switched on automatically by GeneSnap the intensity should be set to maximum to ensure that the lamps strike You can set the intensity to maximum by turning the intensity knob fully clockwise or by disabling it using the bypass switch Fitting the white light pad Note The Epi white light illumination is fitted as standard and no further action on your part is required To fit the white light pad 1 2 5 Remove the white light pad from its packaging Open the Darkroom door push the door up to open it Hold the white light pad with the front towards you and place it on the transilluminator in the Darkroom when placed correctly the
138. ntation RENTALS ITAR CERTIFIED CEP BAD tia Contact us 888 88 SOURCE sales artisantg com www artisantg com
139. ny way both the Processed and Original images will be saved together with any annotations you have placed on them If you reopen the image in GeneSnap you will be able to use View Original or View Processed to view both versions and the annotations will still exist as separate objects that can still be moved or edited as required 8 4 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com File menu Save Image As Note The Save Image As command is disabled when the selected Image window is showing a live image from the camera Note You use Save Image As to save the image in GeneSnap sgd format for Good Laboratory Practice purposes you can reopen images saved in this format in GeneSnap using Open Image You can save images in a wide range of other image formats using Export Image see page 8 6 you will be able to open these images in paint programs or place them in word processor documents but you will not be able to reopen them in GeneSnap When you use Export Image to save an image you can choose whether to save the image with its annotations engraved on it Alternatively you can use Export Image to save the image annotations in a separate file To save the image in the selected Image window to a new image file 1 Choose Save Image As from the File menu to display a standard Windows Save As dialog box Save in 4 Images y
140. ocus greater depth of field if you use a small iris and longer exposure time when you capture the image e f you intend to use Auto Exposure or Series Capture to bracket the exposure you should set the exposure time and iris to give a dark image see Capturing images using Series Capture page 5 7 for more details Focusing As mentioned in the previous section you can focus more easily if you use a wide aperture and short exposure time while you carry out the focusing You can also improve the focusing accuracy by zooming in on some detail setting the focus and then zooming back out to frame the gel as required Saturation detection If you overexpose an image exposure time too long or iris too wide open the lighter parts of the image may be completely white and show no highlight details this is called saturation On the other hand if you underexpose an image exposure time too short or iris too small dark parts of the image may be all black without any shadow details The Show saturated areas button allows you to check whether an image contains any saturated areas areas of the image that are saturated to white are shown in red and any that are saturated to black are shown in blue Saturation mode is particularly useful when you are viewing a live image and adjusting the exposure time and iris settings to get the correct exposure in order to get the best results you should choose an exposure that avoids i
141. of field and vice versa This means that when you are focusing you should use the widest iris setting you can you can reduce the exposure time setting to compensate On the other hand if you want to increase the depth of field when you are capturing the image you should use the smallest iris setting compensated by a larger exposure time setting Zoom controls not GeneGnome or GeneWizard To zoom the camera lens in the Darkroom Press the zoom zoom in or zoom zoom out button in the Image Capture toolbox You use the zoom controls to frame the image but you can also improve the accuracy of focusing by zooming in before focusing and then zooming out to frame the image Focus controls not GeneGnome or GeneWizard To adjust the focus of the camera lens in the Darkroom Image Capture toolbox y Press the focus focus closer or focus focus further away button in the 6 You can increase the accuracy of focusing by zooming in as much as possible and setting the largest iris you can see the previous two sections for more details Biolmaging Systems User Manual 6 7 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com The GeneSnap Application Window Exposure time To set the exposure time 1 Click in the exposure time control in the Image Capture toolbox to select the hours minutes seconds or milliseconds section of the box 00m Hs 000m
142. oh a ea a e n G e oa e a a 8 19 PROPGitles ca Sb doia Ae a weed 8 20 Status Bar se A pd ae Se hid ea ee A 264 A 8 23 WindoW 2 s a co bn 6g eiga aoea d ea Edp a wi e i ae Ee eee eA Re 4 8 24 Cascad oe nei dee ke Eee bee bea A 8 24 THEMOnZONtaly eco ee a we we ee ee ee wwe a 8 24 Tile Verticals seg g e Wk dw ea eh ee eS hoe oe we A eh 8 24 Arrange ICONS ps ea a a we we a a 8 24 Close A nk ek A E Be eR ee go 8 25 Windows open in GeneSnap s s sos o soroa ee Eaa i a e aa 8 25 WOON a es ee oe A ee eee a O ig rs ee ie eee a 8 25 WAR Css Se kh pan ds a AA we e a 8 25 ANNOLE vor ew a eee A ee ee Ge Re a 8 26 ZOOM eaa e BP OR Re ha E amp Bh Ld Pe eS GP 8 26 Standard gs ea oe eS e ad GS ea ow e a Be Ghee 8 26 DU amp 15 ea SG Be NS Oe Ge Wa ME Ge Me OS ee ee ae 8 27 USEF NAMIE y dos Gee ies Eo be ad we doe WP aa ea eR ee 8 27 Report Titles 2 at e oo ae te a RA wy A 8 28 Initial Acquire State s snem a RR RA a 8 28 Save Configurations ss ack a how a ghd a ae BAG a body a ee bd a ge 4 8 29 Delete Configurations lt s ew bebe aed a i eoa ass ood 8 30 Promote Configuration uo 2h ee a eee Red DS ee send 8 31 Autoscale on Capture ee ad e 8 32 IMAGE ae See RRS eH ee ee aH Eee ewe ee a AA 8 33 SKAPET i t ho a Ea eee BE a EE SE we Be SS 8 33 SMOG 4 asd eed etd ee ea aa Beas 8 34 INVERE Ye ceed it i Go ce Ge ey YEG eGo SY wl Ge ie Se a a Dae a 8 34 Flip HOrHZOntal ss suis we ek ee we Ba oh 8 35 Flip Verticals
143. ol from the Image toolbar 2 Click on the annotation To select a group of annotations kR 1 If it is not already selected select the Selector tool from the Image toolbar 2 Press and hold down the mouse button then drag a rectangle around the annotations Any annotations with some part inside the rectangle will be selected To add an annotation to a group of selected annotations or remove one from the group click on the annotation with the Selector tool selected Moving annotations To move one or more annotations 1 Select the annotation s see the previous section 2 Move the pointer over the edge of one of the annotations avoiding any drag handles control points if only one annotation is selected 3 Press and hold down the mouse button then drag the annotation s to the new position Biolmaging Systems User Manual 5 41 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap Aligning annotations To align a group of annotations 1 Select the annotations 2 Right click in the image at the position you want to align the annotations A pop up menu will be displayed Align Left Align Top Align Bottom Align Right 3 Choose the required option Reshaping annotations Note The instructions in this section do not apply to text annotations To reshape an annotation 1 Click on the annotation to select it drag handles con
144. or delivery To fit the top cover 1 Check that none of the cables connected to the camera have come loose during transportation 2 Fit the cover in place and fix it using the screws provided you will need a flat bladed screwdriver Fitting the UV illumination Note If you have purchased the Epi UV illuminator option for GeneGenius it will have been fitted in the Darkroom before delivery and no further action on your part is required The transilluminator is packed separately When fitted in the Darkroom it slides in and out on rails attached to its sides To fit the transilluminator 1 Remove the transilluminator from its packaging Biolmaging Systems User Manual 1 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Introduction and Initial Setup Open the Darkroom door push the door up to open it Take the flying mains lead coming from the inside of the Darkroom and fit it into the mains socket on the back of the transilluminator Holding the transilluminator with its controls towards you locate the rails fixed to the side of the transilluminator into the sliding rails inside the Darkroom Push the transilluminator fully into the Darkroom Make sure that the transilluminator power switch is turned on and the intensity set to maximum see the following paragraph You should read the separate documentation supplied with the transilluminator However there are a few sp
145. or palettes J l Switch to color wash Reset brightness to default Adjust brightness H EL te Reset contrast to default w Adjust contrast F F a Reset Gamma correction B Reset Gamma correction d Reset Gamma correction Adjust Gamma correction qi Adjust Gamma correction T Adjust Gamma correction E Show saturated areas The Show saturated areas button at the bottom of the controls switches Saturation Mode on or off If saturation mode is on any pixels with the maximum value will be shown in red and any pixels with the minimum value will be shown in blue With saturation mode on you can adjust the camera controls so that the brightest and darkest parts of the image almost saturate Gamma correction allows you to adjust the midtones in an image without changing the lightest and darkest tones it determines the shape of the response curve between the black and white points which are fixed by the brightness and contrast settings 6 16 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Image windows Note The image controls only affect the display of the image they do not affect the actual intensity values in the image This may cause problems when you are setting the exposure time or iris to get the best exposure For example if you increase the brightness of the image display of a correc
146. over extended exposures Complete ChemiGenius systems are supplied with e SYNGENE Darkroom fitted with a 12 bit 16 bit performance provided by EDR CCD cooled camera e Motorized zoom lens with close up filter e UV Transilluminator with illuminated area of 20cm x 30cm e White light pad e Epi white light illuminator e Epi UV illuminator e Motorized filter wheel with UV filter other filters available as options e UV protective screen e PC fitted with a framegrabber high resolution monitor keyboard and wheel mouse e Thermal printer e GeneSnap acquisition software e GeneTools match analysis software e Microsoft Office Small Business Edition optional If you have purchased a complete ChemiGenius system from SYNGENE the framegrabber board and all necessary software will have been installed in the PC so all you need to do is connect up the various system components See the appendix at the end of this manual if you have not purchased a complete system Biolmaging Systems User Manual 1 11 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Introduction and Initial Setup Setting up the Darkroom Note Do not connect power to any of the components until you are satisfied that everything is connected correctly for any assistance please contact your supplier or SYNGENE directly Note The motorized filter wheel is standard in ChemiGenius systems
147. ow to e Export images with or without annotations to standard graphics format files e Save annotations into a separate annotations file e Merge annotations from a separate annotations file with the annotations on an image To export the image or save the annotations on the image in the active Image window 1 Choose View Original or View Processed from the View menu depending on whether you want to export the Original or Processed image or the annotations on the Original or Processed image 5 44 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Placing annotations on an image 2 Choose Export Image from the File menu to display the Export Image dialog box Save in Bitmaps el gal ex a Image6 bmp File name Images L E Save as type emp Compressed Cancel F Open as read only T Engrave Annotation I Convert to 16bit IT Gonvertta Bt Z Note The Convert to 8bit check box is disabled in GeneGenius MultiGenius and GeneWizard systems for non EDR images since the images are already 8 bit Similarly Convert to 16bit is always disabled in GeneGnome systems and in EDR images for the other systems since the images are already 16 bit Both check boxes are enabled for ChemiGenius systems 3 Select a folder to hold the exported image or annotations from the Save in drop down list and the file list box
148. owever increasing the brightness control setting has no effect on the image itself and if you were tempted to decrease the exposure the image may become underexposed To avoid these problems always make sure that the image controls are reset to their default positions before deciding whether you need to adjust the iris setting or exposure time You can adjust the display conditions for an individual Image window using e the display controls on the Image window e the Histogram window These are described separately in the following subsections Using the Image window display controls When you display an image in an image window either from a camera or a saved image you can use the display controls attached to the right hand edge of the window to adjust the display brightness and contrast to apply a color wash color washes tint the images to replicate the effect of stains or to use a pseudocolor palette with a pseudocolor palette intensities in the image are represented by different colors Biolmaging Systems User Manual 5 13 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap The following pictures show the function of each of the controls Grayscale Color Wash Pseudocolor Switch to pseudocolor te Switch to grayscale I i Color washes E Pseudocolor palettes E i Switch to color wash Reset brightness to default Adjust bright
149. ows the name of the current Configuration Either Leave the existing name unchanged if you want to update the current Configuration to the current capture settings Or Enter a new name if you want to create a new Configuration with the current capture settings Note If the original Configuration was a system default Configuration you must enter a new name you cannot save changes to a system default Configuration 3 Enter or edit the Description to document the Configuration 4 Press OK to close the dialog box and save the changes to the existing Configuration or create a new user Configuration with the current capture settings Deleting a Configuration To delete a user Configuration you cannot delete a system default Configuration 1 If the Configuration you want to delete is not the current Configuration select it using the Configuration list in the Configuration bar 2 Choose Delete Configuration from the Extras menu You will be asked to confirm that you want to delete the Configuration GeneSnap 2 Do you really want to delete the current configuration 3 Press Yes to delete the Configuration Biolmaging Systems User Manual 5 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap Promoting a user Configuration To promote a user Configuration to be a system default Configuration 1 If the Configuration you want to promo
150. p Chapter 5 and the other reference chapters following it Switching on To switch on the GeneGenius MultiGenius or ChemiGenius 1 Make sure the power leads are connected to a live supply 2 Turn on the Darkroom using the power switch on its back the green power indicator on the front panel will light up 3 Turn on the PC press the on off button for a couple of seconds monitor and printer The PC will take a little time to start up load Windows check that the Darkroom and camera are connected and working and load GeneSnap Biolmaging Systems User Manual 2 1 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneGenius MultiGenius or ChemiGenius When GeneSnap starts up the first time you will be asked to log on GeneSnap User name 1 Type in your name If you have opened GeneSnap before and entered your name you will be able to select it from the drop down list 2 Press OK to open GeneSnap The main GeneSnap Application window see Chapter 6 will open with the Image Capture toolbox displayed on its left hand side HE 00m 00s 040ms A A Epi long wave uv v z Man eriwo E EtBr UV 2 2 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Capturing an image Note The picture shows the Image Captur
151. posure so that the capture cannot be interrupted accidentally The captured images will be shown in separate Image windows You can now inspect the captured images and select the best one for further processing annotation or analysis as required Biolmaging Systems User Manual 2 11 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneGenius MultiGenius or ChemiGenius Capturing an image with Extended Dynamic Range GeneSnap allows you to extend the dynamic range of the cameras in GeneGenius MultiGenius and ChemiGenius to give them 16 bit performance so that you can capture details in the darkest part of the image without having to over expose the brightest parts of the image and lose detail there by saturating them Note An important feature of the EDR process is that the validity of quantitative measurements taken from EDR images is maintained You can use EDR with any of the capture methods described above except Auto exposure To use EDR with one of the capture methods above either Choose an EDR Configuration after Step 1 Gel sample EDR y Check EDR in the Image Capture toolbox See Using EDR Extended Dynamic Range not GeneGnome page 5 10 for more information about EDR Note EDR is not suitable for use with chemiluminescence samples because of the long exposures required due to the low levels of light they emit
152. posure time by pressing the up or down arrow keys on the keyboard or if you are using a wheel mouse by turning the wheel c If required select another section hours minutes seconds or milliseconds and edit that number you can click on the scroll bars at the right hand end of the control to move the selection to the next section E 00m 04s lms Note Only certain values of exposure time are allowed if you type a non allowed value directly into the box it will be corrected to the next allowed value 4 8 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Capturing an image from the camera If you have unchecked Use same exposure for all images in series an additional Image number spin box is displayed in the Series Capture dialog box Number of images in series 5 IV Add contents of previous images to each new image Image number 1 of 5 4 m Exposure control Exposure time E 00m 05s 000ms l Cancel To set the exposure for each image a Click on the up or down arrows next to the Image number spin box to choose an image number b Follow the procedure given in Step 6 for setting the exposure time Note If you have checked Add contents of previous images to each new image the exposure time for the first image will be the exposure set for the first image for the second image
153. power cables to the power sockets on the Darkroom on the back PC monitor and printer See Getting Started with GeneGenius MultiGenius and ChemiGenius Chapter 2 for how to switch on the system and use it to capture images Biolmaging Systems User Manual 1 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Introduction and Initial Setup MultiGenius Overview MultiGenius is a comprehensive and fully automated gel documentation and analysis system It features some extremely advanced concepts in image acquisition and processing and is ideal for laboratories working with all types of gel media including DNA gels protein gels autoradiographs and chemiluminescence The MultiGenius system uses a Peltier cooled CCD camera so that you can use the extended exposures required for chemiluminescence samples without excessive noise Complete MultiGenius systems are supplied with e SYNGENE Darkroom fitted with an 8 bit 16 bit performance provided by EDR CCD cooled camera e Motorized zoom lens with close up filter e UV Transilluminator with illuminated area of 20cm x 20cm optional 20cm x 30cm version e White light pad e Epi white light illuminator e Epi UV illuminator optional e Motorized filter wheel with UV filter other filters available as options e UV protective screen e PC fitted with a framegrabber high resolution monitor keyboard and mouse e Thermal prin
154. program on your PC It also has a link to the SynGene web site Biolmaging Systems User Manual 8 39 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Menus 8 40 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Appendix PC Board and Software Installation If you have not purchased a complete system from SYNGENE you will need to install the framegrabber board GeneGenius or MultiGenius system or Firewire board ChemiGenius and supporting software in your PC To install a board you will need a free PCI slot in the PC The recommended installation order is e GeneTools e Framegrabber or Firewire board e GeneSnap Installing GeneTools To install GeneTools 1 Place the GeneTools installation CD ROM in the PC s CD ROM drive 2 The GeneTools CD Guide will be displayed automatically if it isn t repeat Steps 2 and 3 in the previous instructions but at Step 3 enter d cdguide 3 Press Install 4 Follow the instructions on screen 5 At the end of the installation procedure the first Install Wizard Your installation dialog box will be displayed so that you can request a security key from SYNGENE 6 Enter the Media Key supplied with the software and if required edit the Name and Organization Biolmaging Systems User Manual Appendix 1 Artisan Technology Group
155. r providing powerful and time saving alternatives for full details of these and the many other features offered by GeneSnap see Using GeneSnap Chapter 5 and the other reference chapters following it Switching on To switch on the GeneWizard 1 Make sure the power leads are connected to a live supply 2 Turn on the main GeneWizard power switch this is a rocker switch just above the power input socket on the back of the GeneWizard 3 Press the processor on off button for a couple of seconds looking at the back of the GeneWizard this is a black push button switch at the top right hand corner of the back panel 4 Turn on the monitor The GeneWizard will take a little time to start up while it loads Windows and then GeneSnap Biolmaging Systems User Manual 4 1 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneWizard When GeneSnap starts up the first time you will be asked to log on GeneSnap User name 1 Type in your name If you have opened GeneSnap before and entered your name you will be able to select it from the drop down list 2 Press OK to open GeneSnap The main GeneSnap Application window see Chapter 6 will open with the Image Capture toolbox displayed on its left hand side j 00m 00s 040ms Transilluminator ha a 4 2 Biolmaging Systems User Manual Artisan Technology Group Quality Inst
156. r on the corners and in the middle of the sides of its bounding rectangle so that you can move or reshape the ellipse Note You can select the Select tool when the Draw Ellipse tool is selected by pressing the Select button on the Annotate toolbar Drawing a freehand shape To draw a freehand shape annotation on an image Lad 1 Choose whether to draw a filled or hollow freehand shape press the Hollow Filled Shape button if the Draw Freehand Shape button shows the wrong sort of freehand shape 2 Press the Draw Hollow Freehand Shape button or Press the Draw Filled Freehand Shape button A 5 32 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Placing annotations on an image Note You can draw a freehand shape as a series of straight line segments or completely freehand or as a mixture of the two As an example the following instructions show you how to draw a freehand shape by drawing a series of straight line segments followed by a freehand section and finishing with a final straight line segment back to the start point 3 Move the pointer to the position where you want to start the freehand shape When the Draw Freehand Shape tool is selected the pointer changes to a pencil when it is over the image Se Nae oe 4 Click to place the start of the first line segment in the freehand shape it will be marked
157. r printer s documentation for details Check Print to file if you want to send the printer output to a file rather than directly to a printer If you choose this option you will be prompted to give a file name for the output when you press OK Select the All radio button if you want to print all the pages in the report select the Pages radio button and enter the start from and end to pages if you only want to print a range of pages Enter the Number of copies of the report that you want to print Press OK to close the dialog box and send the output to the printer or display a dialog box so that you can enter a name for the file if you are printing to a file Most recently used files Exit Near the bottom of the File menu there is a list of the files you have opened or saved most recently To reopen one of the most recently used files Choose its name from the File menu Note You cannot exit GeneSnap while an Image window is showing a live image To exit GeneSnap Choose Exit from the File menu If there are any Image windows containing unsaved grabbed images from the camera or if you have made any changes to images since they were last saved you will be asked if you want to save the changes Biolmaging Systems User Manual 8 15 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Menus Edit Cut Copy Paste Cut Ctrl x Copy Ctrl C Pa
158. re toolbox By default the Image Capture toolbox is docked on the left hand side of the GeneSnap Application Window However you can make it float freely on the desktop or dock it to another edge of the window To float the Image Capture toolbox 1 Move the pointer over the drag bars at the edge of the Image Capture toolbox Y e R 2 Drag the toolbox away from the edge Note You can also float the Image Capture toolbox by double clicking on the drag bars it will be restored to the position it held when it was last floating Note When the Image Capture toolbox is floating you can close it by clicking on the close button at its top right hand corner see the previous section for how to display it again To dock the Image Capture toolbox against an edge of the GeneSnap Application Window Drag the Image Capture toolbox by its title bar and drop it on the edge Note You can also dock the Image Capture toolbox by double clicking on its title bar it will be docked on the same edge as when it was last docked 6 4 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Image Capture toolbox Door drawer icons The icon in the Image Capture toolbox shows for GeneGenius MultiGenius and ChemiGenius whether the Darkroom s door is open closed or locked the door is locked during exposures longer than 30 se
159. romote to System Default Configuration x Current System Configurations Gel sample Gel sample EDR New Name Description Note The list box at the top of the dialog box shows all the Current System Configurations the list does not include your user Configurations 3 If you want to change the name of the Configuration when it is promoted edit the name in the New Name box Note The original user Configuration will be removed even if you enter a new name for the promoted Configuration Biolmaging Systems User Manual 8 31 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Menus 4 If required edit the Description the description of the selected Configuration is displayed in a tooltip when you hold the pointer over it in the Configuration toolbar 5 Press OK to confirm that you want to promote the Configuration Once you have promoted a user Configuration to be a system default Configuration it will be available to all users on the PC Note You can change the capture settings while you are using a system default Configuration but if you then try to save the Configuration you will have to enter a new name and it will be saved as a new user Configuration Autoscale on capture To choose whether the new windows created when you capture an image should be in fixed magnification or autoscale zoom to fit mode Choose Autoscale on c
160. ropriate chapter in the Getting Started chapter for your system to find out how to turn it on and start working productively with it The first chapter in the Reference part of the manual Using GeneSnap builds on the Getting Started chapters and goes into rather more depth showing you alternative ways of proceeding and more advanced features The remaining chapters in the Reference part of the manual provide a systematic reference to the GeneSnap software 1 20 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Part 2 Getting Started Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneGenius MultiGenius or ChemiGenius This chapter gives a quick introduction to using your GeneGenius MultiGenius or ChemiGenius system taking you through the processes of starting up capturing the image and opening the image in GeneTools for analysis The final section of the chapter gives some further hints on using GeneGenius MultiGenius and ChemiGenius There are other ways to carry out the operations described in this chapter providing powerful and time saving alternatives for full details of these and the many other features offered by GeneSnap see Using GeneSna
161. rresponding Invert check box es 8 10 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com File menu 5 Check Create monochrome image if you want the composite image to be monochrome rather than color so that it appears similar to a normal captured image The composite image will be displayed in monochrome in the dialog box if you check the box 6 Check Balance maximum values in each color plane to weight the contributions of each image according to the maximum values in each see next paragraph for details of why you may want to do this If you do not select this option when GeneSnap creates a composite image it takes equal contributions from each component image However this can cause problems if one of the images is much lighter or darker than the other s or if the images are a mixture of EDR 16 bit and non EDR 8 or 12 bit images Balancing the maximum values in each color plane avoids these problems 7 Press OK to create the composite image The new composite image will be created and displayed in a new Image window You can apply any of GeneSnap s operations to the composite image in the same way as for a captured image In particular you can save the composite image and analyze it in GeneTools However you should note that the results of analyzing a composite image do not satisfy the conditions required for Good Laboratory
162. rumentation Guaranteed 888 88 SOURCE www artisantg com Capturing an image from the camera Capturing an image from the camera This section shows you how to carry out some typical procedures for capturing images You will learn how to e Capture an image using an automatic exposure see page 4 4 e Capture an image from live video see page 4 5 e Capture a series of images see page 4 6 e Capture an image with Extended Dynamic Range see page 4 10 Once you have understood these examples you will be able to choose and if necessary modify the technique that best suits your own requirements and the samples you are using Whichever technique you use the first task is to insert the sample Since this procedure is common to all the capture techniques it is described before the separate procedures Inserting the sample To insert the sample 1 Prepare the sample 2 If you have just switched on the GeneWizard the sample drawer at the bottom of the GeneWizard will be unlatched and you should open it by pulling it towards you Note Keep hold of the drawer and pull carefully to avoid pulling the drawer completely out of the GeneWizard If the sample drawer is closed this will be shown on the graphic in the Image Capture toolbox and the Open drawer button will be enabled Biolmaging Systems User Manual 4 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE w
163. s 2 Type the new value over the numbers or click on the up or down spin arrow at the left hand end of the control to increase or decrease the number OOmUE s 000ms Note You can also increase or decrease the exposure time by pressing the up or down arrow keys on the keyboard or if you are using a wheel mouse by turning the wheel 3 If required select another section hours minutes seconds or milliseconds and edit that number you can click on the scroll bars at the right hand end of the control to move the selection to the next section E 00m 04s is IN Note Only certain values of exposure time are allowed if you type a non allowed value directly into the box it will be corrected to the next allowed value The allowed values depend on the system you are using Automatic exposure not GeneGnome To capture an image from the camera using an automatically determined exposure a Press the Automatic exposure button in the Image Capture toolbox See page 5 10 for further details 6 8 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Image Capture toolbox Image series To capture a series of images from the camera using identical or individually set exposures Press the Image series button in the Image Capture toolbox See page 5 7 for further details Lighting control not GeneGnome Transilluminator Ka
164. s match analysis software Microsoft Office Small Business Edition optional The GeneGnome system is supplied complete and with all necessary software installed in the PC so all you need to do is to connect the keyboard mouse and monitor Connecting up the System To connect the GeneGnome system components 1 Unscrew the knurled fixing screw holding the cover plate on the left hand side of the GeneGnome 2 Remove the cover plate to reveal the connectors beneath 3 Plug in the monitor keyboard and mouse leads the sockets are labelled with appropriate icons Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com GeneWizard Note You should also connect any optional accessories you have purchased such as a printer to the appropriate connectors beneath the cover panel 4 Refit the cover panel slotting the cables through the cutouts and replace the knurled fixing screw to hold it in place 5 Connect power cables to the power sockets on the GeneGnome on the back and monitor See Getting Started with GeneGnome Chapter 3 for how to switch on the GeneGnome and use it to capture images GeneWizard Overview GeneWizard is an affordable fully automated gel documentation and analysis system It features 16 bit performance with many outstanding features usually only associated with advanced systems Standard GeneWizard s
165. s of illumination For example a chemiluminescence sample requiring no illumination with a non chemiluminescent molecular weight standard track requiring white light GeneSnap allows you to cope with this situation by capturing images under different illumination conditions and then combining them to form a composite image which can be analyzed in exactly the same way as if it were a single exposure To create a new composite image from two or three other images 1 Capture or open the images you want to superimpose The Create new composite image command is disabled unless two or more images are open in GeneSnap Note Take care not to move the gel between captures Biolmaging Systems User Manual 5 19 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap 2 Choose Create new composite image from the File menu to display the Create NON GLP Composite Image dialog box Create NON GLP Composite Image None leave blank None leave blank None leave blank The three color drop down list boxes at the top of the dialog box each list the currently open images together with the None leave blank item 3 Select the two or three images you want to superimpose from the color drop down list boxes When you select the first image it will be displayed in the dialog box in the list box color When you select the second
166. s on the GeneWizard on the back and monitor See Getting Started with GeneWizard Chapter 4 for how to switch on the GeneWizard and use it to capture images 1 18 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Software overview Software overview This section gives an overview of the software supplied with all the Biolmaging systems described in this manual GeneSnap You use the GeneSnap program to control the hardware to capture images and to process the captured images In GeneGenius MultiGenius and ChemiGenius systems you can use GeneSnap to control the Darkroom illumination focusing zooming iris setting and exposure length while viewing a live image from the camera You can use GeneSnap to capture images e from a live image not GeneGnome e asa single frame capture e in a series with the same or variable exposures e using auto exposure not GeneGnome The patented Extended Dynamic Range EDR feature allows you to extend the dynamic range of the system s camera not GeneGnome In particular it increases the detail in low intensity areas of the image allowing you and analysis software like GeneTools to distinguish features in dark parts of the object that would otherwise be undetectable without saturating the lighter areas A histogram display allows you to maximize the image contrast without losing any deta
167. sed When you close the door the selected lighting will turn on automatically The system is now ready to capture an image using one of the techniques in the following sections Capturing an image using automatic exposure You can use this capture procedure in GeneGenius MultiGenius or ChemiGenius and GeneWizard but not GeneGnome You can use automatic exposure with any type of illumination Note Because of the long exposures required you should not use autoexposure for chemiluminescence samples Biolmaging Systems User Manual 2 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneGenius MultiGenius or ChemiGenius To carry out an image capture using an automatic exposure 1 Follow the procedure in Framing and focusing the image see page 2 3 to prepare the system for capturing an image 2 Select the appropriate configuration for the sample you are using from the drop down list box in the Configuration bar at the top of the GeneSnap window This sets the lighting and filter and the camera resolution in ChemiGenius systems Note If you want to use other settings you can change the settings or options manually ag 3 Press the Automatic exposure button in the Image Capture toolbox Note When you are using auto exposure the iris should be set so that there are no saturated areas in the image when the exposure is set
168. series captured with the set exposure 4 Check Use same exposure for all images in series if you want to set a single exposure for all images Note If you check both Use same exposure for all images in series and Add contents of previous images to each new image the exposure time for the first image will be the set exposure for the second image the effective exposure time will be 2x the set exposure for the third it will be 3x the set exposure and so on Uncheck Use same exposure for all images in series if you want to set a separate exposure for each of the images Biolmaging Systems User Manual 3 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneGnome 5 If you have checked Use same exposure for all images in series you can adjust the exposure time as follows a Click in the exposure time control to select the hours minutes seconds or milliseconds section of the box 01m iis 000ms b Type the new value over the numbers or click on the up or down spin arrow at the left hand end of the control to increase or decrease the number 01mElls 000ms Note You can also increase or decrease the exposure time by pressing the up or down arrow keys on the keyboard or if you are using a wheel mouse by turning the wheel c If required select another section hours minutes seconds or milliseconds and edit that number you can
169. splay the Capture page View Properties The Capture page shows the capture settings when the image was captured you cannot change this information 8 22 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com View 4 Click on the Notes tab to display the Notes page View Properties x Description User Fields Capture Enter or edit text on the Notes page to document the image the text will be stored with this individual image and can be printed out with the image in a report 5 Press OK to close the dialog box and save any additions or changes you have made Status Bar To show or hide the Status Bar at the bottom of the GeneSnap Application window Choose Status Bar from the View menu The command is checked in the menu when the Status Bar is shown Biolmaging Systems User Manual 8 23 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Menus Window Cascade Tile Horizontal Tile Vertical Arrange Icons Close All v 1 Image6 sqd 001 2 mage3 sqd Note The Window menu is hidden when no Image window is open Cascade To resize and arrange the open non minimized Image and Browser windows so that they are overlapping with their title bars visible Choose Cascade from the Window menu Tile Horizontal To arrange a
170. ste Ctrl V Undo Ctrl 2 To copy the selected annotation to the Windows clipboard and remove it from the image Choose Cut from the Edit menu To copy the selected annotation to the Windows clipboard and leave it on the image Choose Copy from the Edit menu To place a copied annotation on the image in the selected Image window Choose Paste from the Edit menu The annotation will be pasted in the same position as it was copied from This means that if you are pasting to the original image and you have not moved or removed the original annotation it will be pasted on top of the original so you may not notice any change However you will be able to drag the copy to move it away from the original Note If you copy an annotation from the bottom right hand corner of a large image and paste it onto a smaller image it will not appear if its original position was completely outside the image area of the smaller image Undo When you make major changes to an image in particular when you smooth sharpen flip invert or emboss it GeneSnap maintains a copy of the processed image before it makes the change This allows you to undo the change by reverting to the copy 8 16 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com View To undo the most recent major change to an image Choose Undo from the Edit menu Note I
171. t to use the transilluminator you can stow the white light pad out of the way in the Darkroom without disconnecting it To do this lift the white light pad up at the front until it is nearly vertical and then slide it down into the clips at the back of the Darkroom Connecting up the System To connect up a complete GeneGenius system 1 Connect the monitor keyboard and mouse to the labelled sockets on the back of the PC Note At this stage you may want to connect the PC to the power and turn it on to check that it is working correctly If you do this the GeneSnap log on dialog box will be displayed after Windows has opened press Cancel to close GeneSnap When you are satisfied that the PC is working correctly close down Windows switch off the PC and disconnect it from the power supply before proceeding to the next step 2 Connect the thermal printer to a USB socket on the back of the PC The USB plug can only be inserted one way round 3 Use the supplied braided cable with 25 way connectors on each end to connect the socket labelled DR1 on the back of the PC to the DR1 socket on the Darkroom 4 Use the supplied serial Darkroom cable with 9 pin connectors on each end to connect one of the Com port sockets on the back of the PC labelled Com 1 or Com 2 to the Com 1 socket on the Darkroom The cable can only be connected one way round as the connectors at each end are different 5 Connect
172. tart working with GeneWizard Starting GeneSnap GeneSnap starts automatically when you turn on the PC However if you close it for any reason you can restart it without having to restart the PC by double clicking on the GeneSnap icon on the Windows Desktop YE ia GeneSnap from SynGene Biolmaging Systems User Manual 4 11 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneWizard Logging in If you do not want to display the log in dialog box automatically when the program starts uncheck the Show this dialog box at program start box GeneSnap User name Eg User Name T Show this dialog at program start Remove User coca The last user will be logged in automatically when the program starts You can use User name in the Extras menu to log in a different user and or choose to display the log in dialog box on program start up again Displaying the Image Capture toolbox To display the Image Capture toolbox if it is not displayed Image display Press the camera button in the Standard toolbar Depending on the display mode of the PC the Image window may only show a restricted number of gray shades even though the captured 16 bit image contains much more information This means that you may need to adjust the display in the image window to view the detail you require see Adjusting display conditions page 5 13 for
173. tate the image by a user defined angle This is because each of the pixels in the new image would overlap several pixels in the original image So the value in each new pixel would need to be calculated in some way from the values in the overlapped original pixels This recalculation process would then bring into question the validity of any analysis Note You can also add annotations over an image see page 5 27 for details Note When you make major changes to an image in particular when you smooth sharpen flip invert or emboss it GeneSnap maintains a copy of the processed image before it makes the change This allows you to choose Undo from the Edit menu to revert to the copy See Undo page 8 16 for more details Image toolbar All of the operations described in this section except embossing can be carried out using tools in the Image toolbar To display the Image toolbar if it is not already displayed Choose Image from the Tools menu Image is checked in the Tools menu when the Image toolbar is displayed Note Displaying the Image toolbar automatically hides the annotation toolbars Choose Image from the Tools menu 5 22 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Manipulating images If you do not want to display the Image toolbar there are menu equivalents for all the operations exc
174. tation supplied with the transilluminator However there are a few specific points you should note There are three controls on its front from left to right these are a knob controlling the UV intensity a switch to bypass the intensity control and a master on off switch When you switch on the UV light or when it is switched on automatically by GeneSnap the intensity should be set to maximum to ensure that the lamps strike You can set the intensity to maximum by turning the intensity knob fully clockwise or by disabling it using the bypass switch Fitting the white light pad Note The Epi white light illumination is fitted as standard and no further action on your part is required To fit the white light pad 1 2 Remove the white light pad from its packaging Open the Darkroom door push the door up to open it Hold the white light pad with the front towards you and place it on the transilluminator in the Darkroom when placed correctly the white light pad s power supply socket is on the left hand side and towards the back Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ChemiGenius 4 Take the flying low voltage power supply lead coming from the inside of the Darkroom and fit it into the white light pad s power supply socket 5 Make sure the power button on the side of the white light pad is turned on This
175. te is not the current Configuration select it using the Configuration list in the Configuration bar Note If you make any changes to the capture settings after selecting the Configuration you want to promote the changed settings not the original ones will be saved in the promoted Configuration 2 Choose Promote Configuration from the Extras menu to display the Promote to System Default Configuration dialog box Promote to System Default Configuration x Current System Configurations Gel sample Gel sample EDR New Name Long wave EPI Description Note The list box at the top of the dialog box shows all the Current System Configurations the list does not include your user Configurations 3 If you want to change the name of the Configuration when it is promoted edit the name in the New Name box Note The original user Configuration will be removed even if you enter a new name for the promoted Configuration 4 If required edit the Description 5 Press OK to confirm that you want to promote the Configuration 5 4 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Capturing images from the camera Once you have promoted a user Configuration to be a system default Configuration it will be available to all users on the PC You cannot delete or edit a system default Configuration using GeneSnap Not
176. teed 888 88 SOURCE www artisantg com File menu Report Settings To choose what information to include in printed reports 1 Choose Report Settings from the File menu to display the GeneSnap Report Settings dialog box GeneSnap Report Settings x m Report detail Plain d T Include full capture setting C Print image with summary information Print image only Video Printer output C Print full page image with heading Print full page image only 2 Click on the radio button for the amount of detail you want to include in the report For a full report you can choose to include full details of capture settings by checking the check box Note If you want to print to a thermal printer select one of the Video Printer output options 3 Press OK to confirm your choice and close the dialog box Note See Report Titles in the Extras menu page 8 28 for how to set the text to appear at the top of full reports see Print in the File page 8 14 for how to print reports Print Preview To preview a printout of the image in the selected image window Choose Print Preview from the File menu Biolmaging Systems User Manual 8 13 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Menus Print The Image window will switch to preview mode with a preview button bar at the top wo Pade fi
177. ter e GeneSnap acquisition software e GeneTools match analysis software e Microsoft Office Small Business Edition optional If you have purchased a complete MultiGenius system from SYNGENE the framegrabber board and all necessary software will have been installed in the PC so all you need to do is connect up the various system components See the appendix at the end of this manual if you have not purchased a complete system Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com MultiGenius Setting up the Darkroom Note Do not connect power to any of the components until you are satisfied that everything is connected correctly for any assistance please contact your supplier or SYNGENE directly Note The motorized filter wheel is standard in MultiGenius systems and will have been fitted in the Darkroom before delivery together with any additional filters you have purchased Fitting the camera For MultiGenius systems the Darkroom is supplied with the top cover removed and the camera lens assembly unmounted for delivery so you will need to fit them to the Darkroom The camera is supplied with zoom lens and close up lens already fitted to it Note The camera lens assembly is a sensitive instrument and must be handled with care at all times In particular you should take care to avoid touching the lens surface
178. the detail you require see Adjusting display conditions page 5 13 for details It is important to note that this does not change the information that has been captured just the way it is viewed Saturation detection Because GeneGnome captures and saves 16 bit images it has a very wide dynamic range which means that higher levels of light can be detected before it reaches saturation point To check for image saturation Press the Show saturated areas button in the image control bar at the right hand edge of the image window When saturation mode is on any areas of the image that are saturated to white are shown in red and any that are saturated to black are shown in blue This enables you to determine whether any details in important areas of the image are being lost because of saturation Note It is important to make sure that the image brightness and contrast controls are set to their default positions before using saturation mode to decide whether you need to adjust the exposure time see the note at the start of Adjusting display conditions page 5 13 for more details When saturation mode is on the Show saturated areas button is shown as depressed To switch saturation mode off Press the Show saturated areas button again You can also judge the degree of saturation by displaying the Histogram window 3 10 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guar
179. the effective exposure time will be the exposure time set for the first image plus the exposure time set for the second image for the third image it will be the sum of the exposure times set for the first three images and so on 7 Press OK to confirm your selections close the dialog box and start the image capture The captured images will be shown in separate Image windows By taking a series of exposures of different lengths you can bracket the expected exposure with longer and shorter exposure times and then choose the best image from the series You can now inspect the captured images and select the best one for further processing annotation or analysis as required Biolmaging Systems User Manual 4 9 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneWizard Capturing an image with Extended Dynamic Range GeneSnap allows you to extend the dynamic range of the GeneWizard camera to give it 16 bit performance so that you can capture details in the darkest part of the image without having to over expose the brightest parts of the image and lose detail there by saturating them Note An important feature of the EDR process is that the validity of quantitative measurements taken from EDR images is maintained You can use EDR with any of the capture methods described above except Auto exposure To use EDR with one of the capture met
180. tly exposed image the light parts of the image will eventually become saturated and be shown in red if the Show saturated areas button is depressed This may tempt you to decrease the exposure time which would lead to underexposure To avoid these problems always make sure that the image controls are reset to their default settings when you are adjusting the exposure time and or iris setting to get the best exposure Note You can also adjust the brightness and contrast of the image display using the cursors in the Histogram window see page 6 18 Original and Processed View modes In order to protect your data GeneSnap does not allow you to change the image values in the original image Therefore when you carry out an operation that changes the image values GeneSnap makes a copy of the Original image and changes the values in the copy This Processed image is then displayed in the Image window in place of the original However the Original image is still associated with the image window and you can choose between showing the Processed image or the Original image in the Image window To switch the selected Image window to View Original mode Choose View Original from the Image menu To switch the selected Image window to View Processed mode Choose View Processed from the Image menu The command is disabled if there is no Processed image associated with the selected Image window If you carry out another op
181. to create system default Configurations However once you have promoted one of your user Configurations you will not be able to edit it Selecting a Configuration Note You cannot change the Configuration while GeneSnap is displaying a live image To select a new Configuration and set the current capture settings to the values saved in the Configuration Choose the required Configuration from the drop down list box in the Configuration toolbar Shor wave EPI y Note The drop down list box lists all your user Configurations together with any system default Configurations on the PC see User and system default Configurations page 5 1 Creating and saving Configurations To create and save a new user Configuration containing the current capture settings or save changes in an existing user Configuration 1 Choose Save Configuration As from the Extras menu to display the Save Configuration dialog box Save Configuration Current User Configurations wave EPI Save As Description 5 2 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Working with Configurations Note The list box at the top of the dialog box shows all your Current User Configurations the list does not include any system default Configurations on your PC see User and system default Configurations page 5 1 2 The Save As box sh
182. trol points will appear on the annotation 2 Move the pointer over the drag handle control point you want to move 3 Press and hold down the mouse button then drag the handle control point to its new position Deleting annotations To delete an annotation 1 Click on the annotation to select it 2 Press DEL 5 42 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Placing annotations on an image Copying annotations To copy one or more annotation s to the same image 1 Select the annotation s see page 5 41 2 click on an annotation Copies of all of the selected annotations will be created on top of the originals To copy one or more annotation s to the same or another image 1 Select the annotation s 2 Choose Copy from the Edit menu 3 Select the Image window that you want to copy to 4 Choose Paste from the Edit menu The copied annotation s will be pasted in the same position s on the image as the original s Editing text annotations To edit the text in a text annotation 1 Click on the annotation to select it drag handles control points will appear around the text to show it is selected Note You can select the text annotation with either the Selector tool or Draw Text tool 2 Click again to place a flashing cursor in the text 3 Edit the text using the keyboard To change the text or
183. trumentation Guaranteed 888 88 SOURCE www artisantg com Introduction and Initial Setup Introduction This manual gives full instructions for setting up and using the following SYNGENE Biolmaging systems e GeneGenius e MultiGenius e ChemiGenius e GeneGnome e GeneWizard The manual includes full instructions for using the GeneSnap software The manual is divided into three parts Introduction and setup this chapter Getting Started and Reference The next three main sections in this chapter treat each system in turn giving a brief overview and then a description of how to connect up the system components The final main section of the chapter gives an overview of the software which is common to all the systems The Getting Started part of the manual again deals with each system in turn GeneGenius MultiGenius and ChemiGenius are described together in a single chapter since the procedures described are identical separate chapters show you how to get started with GeneGnome and GeneWizard Each chapter takes you through basic procedures for capturing an image and sending it to GeneTools for analysis The first chapter in the Reference part of the manual Chapter 5 Using GeneSnap describes some other methods for capturing images and shows you how to control the way images are displayed It then shows you how to work with captured images for presentation purposes including how to enhance them using a variety of
184. ts This section gives a few further hints to help you start working with GeneGnome Starting GeneSnap GeneSnap starts automatically when you turn on the PC However if you close it for any reason you can restart it without having to restart the PC by double clicking on the GeneSnap icon on the Windows Desktop Xd t s ie GeneSnap from SynGene Logging in If you do not want to display the log in dialog box automatically when the program starts uncheck the Show this dialog box at program start box GeneSnap User name x User Name TF Show this dialog at program start Remove User coca The last user will be logged in automatically when the program starts You can use User name in the Extras menu to log in a different user and or choose to display the log in dialog box on program start up again Displaying the Image Capture toolbox To display the Image Capture toolbox if it is not displayed ver Press the camera button in the Standard toolbar Biolmaging Systems User Manual 3 9 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneGnome Image display Depending on the display mode of the PC the Image window may only show a restricted number of gray shades even though the captured 16 bit image contains much more information This means that you may need to adjust the display in the image window to view
185. ttom of the compartment with the connector outside the compartment Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ChemiGenius 4 Slide the control box into the control box compartment from the rear of the Darkroom it should slide in to make a snug fit with all its connections exposed at the rear Make sure that the flying power lead does not get pushed into the Darkroom 5 Connect the flying power lead to the power socket on the control box 6 Connect the camera cable to the socket on the control box and secure the connector in place with the locking screws 7 Fix the control box compartment cover in position fitting the cables into the cable slots so that they are secured in place 8 Making sure that the plastic spacer ring is fitted between the lens and the Darkroom with the groove in the ring facing away from the camera attach the camera lens assembly in the Darkroom inside the darkroom using the two brackets provided one bracket attaches to the camera the other to the lens Do not tighten the lens screw more than finger tight Note It is VERY IMPORTANT to make sure that the plastic spacer ring is fitted correctly between the lens and the Darkroom if the spacer is not fitted the Darkroom and or camera will be damaged 9 Fit the wide grey camera power cable coming from the control box to the c
186. tton to start GeneTools with the image in the selected Image window loaded if the image has not been saved you will be prompted to save it first using a Save As dialog box Note If you have processed the image in any way the image file will contain a Processed image in addition to the Original image in accordance with good laboratory practice GeneTools will always analyze the Original image 7 8 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Configuration There is no menu command equivalent to pressing this button Show Histogram Window dl Pressing the Show Histogram Window button is equivalent to choosing Histogram from the View menu to view the Histogram window which shows the distribution of intensities in the image in the selected Image window See page 6 18 for more information about the Histogram window Context sensitive Help he Pressing the Context sensitive Help button changes the pointer into the Help pointer R You can use this to select a menu command or click on an area of the window to display Help for the selected item There is no menu command equivalent to pressing this button Configuration Short wave EPI The Configuration toolbar contains a drop down list box listing the Configurations that you can use Selecting a Configuration from the list sets the current capture settings to the val
187. ues saved in the Configuration Note You cannot change the Configuration while GeneSnap is displaying a live image See Working with Configurations page 5 1 for more information about working with Configurations Biolmaging Systems User Manual 7 9 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Toolbars 7 10 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Menus File menu Note Some File menu commands are hidden when no Image window is open Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Menus New Image Note The New Image command is disabled if there is already an Image window showing a live image from the camera To open a new Image window showing an image from the camera E You can use Initial Acquire State in the Extras menu see page 8 28 to choose whether a new Image window should be opened automatically showing a live image Choose New Image from the File menu from the camera when GeneSnap opens Open Image To open a previously saved image in a new Image window a Choose Open Image from the File menu to display a standard Windows Open dialog box Look in E Images Y Al cH Image6 sad Files of type Sy
188. ur CD ROM is not the d drive Follow the instructions given on the screen Appendix 4 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Installing GeneSnap Checking the driver installation in Windows 95 98 XP Pro If you have a problem after installing GeneSnap you should check that the driver has been installed correctly To check that the driver has been recognised correctly by Windows 1 Press the Start button in the Windows task bar and choose Control Panel from the Start gt Settings submenu to display the Control Panel Double click the System icon Click on the Device Manager tab Click on View devices by type if it is not already selected Open the Sound Video and Game Controllers item Confirm that there is an entry for e Synoptics Prymo Grabber GeneGenius or MultiGenius system e Generic ChemiGenius on Windows XP Pro right click on the entry choose Properties to display dialog box showing Synoptics CG2 1 e Synoptics CG2 1 ChemiGenius on other systems Confirm that there are no conflicts or other problems these are shown by a yellow exclamation mark next to the entry Disabling drivers in Windows NT If at any time you remove the framegrabber GeneGenius or MultiGenius system or Firewire ChemiGenius board Windows NT will display error messages when it starts up If this happens you should d
189. ut the Histogram window Grid on Live To choose whether to show or hide a grid over live images Choose Grid on Live from the View menu Grid on Live is checked in the View menu when the option is selected Displaying a grid on a live image can help you adjust the position of the gel so that the tracks are parallel to the edges of the image this makes it easier to apply annotation overlays to the image and can also make analysis more straightforward Normal 1 1 To return the view of the image in the selected Image window to the normal 1 1 magnification state e Choose Normal 1 1 from the View menu 8 18 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com View Zoom In To produce a more magnified view of the image A Choose Zoom In from the View menu You can also zoom in to an image using a wheel mouse by holding and spinning the wheel away from you See Zooming and scrolling Image windows pages 6 13 6 15 for information about using the overview to scroll a zoomed image Zoom Out To produce a less magnified view of the image e Choose Zoom Out from the View menu You can also zoom out from an image using a wheel mouse by holding and spinning the wheel towards you View Original To switch the selected Image window to View Original mode Choose View Original from the Image menu See Original and Processed View
190. w to place annotations on an image The annotations are stored separately from the image and do not affect the information stored in the image You can apply annotations separately to the Original and Processed images When you export an image to a standard graphics file you can choose whether to include the annotations if you do they will be engraved on the image in other words the annotation will become part of the graphic itself replacing any underlying image information see Exporting images and engraving saving and merging annotations on page 5 44 for details Annotate toolbar The operations described in this section for placing annotations on an image are carried out using tools in the Annotate toolbar RN NOORANKN ld To display or hide the Annotate toolbar together with the Color and Line Style toolbars Choose Annotate from the Tools menu Annotate is checked in the Tools menu when the annotation toolbars are displayed Biolmaging Systems User Manual 5 27 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using GeneSnap Note Displaying annotation toolbars automatically hides the Image toolbar There are no menu equivalents for the operations carried out using the Annotate toolbar Showing and hiding annotations To show or hide the annotations on an image Choose Annotation from the View menu the command is checked in the m
191. white light pad s power supply socket is on the left hand side and towards the back Take the flying low voltage power supply lead coming from the inside of the Darkroom and fit it into the white light pad s power supply socket Make sure the power button on the side of the white light pad is turned on This is how the white light pad should be located when you are using it If you want to use the transilluminator you can stow the white light pad out of the way in the Biolmaging Systems User Manual 1 9 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Introduction and Initial Setup Darkroom without disconnecting it To do this lift the white light pad up at the front until it is nearly vertical and then slide it down into the clips at the back of the Darkroom Connecting up the System To connect up a complete MultiGenius system 1 Connect the monitor keyboard and mouse to the labelled sockets on the back of the PC Note At this stage you may want to connect the PC to the power and turn it on to check that it is working correctly If you do this the GeneSnap log on dialog box will be displayed after Windows has opened press Cancel to close GeneSnap When you are satisfied that the PC is working correctly close down Windows switch off the PC and disconnect it from the power supply before proceeding to the next step 2 Connect the thermal printer to a
192. will be empty until the selected filter is in position Image windows E demoj1 sgd 003 Image windows can show live video images from a camera not GeneGnome captured images or images loaded from files 6 12 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Image windows Image windows are standard Windows document windows which you can minimize restore move and resize in the normal way You can use commands in the Window menu to tile the non minimized Image windows and Browser if it is not minimized see page 6 22 for more about the Browser cascade them and if they are minimized arrange their icons You can select an Image window or the Browser in the usual way by clicking in it if it is visible or by selecting its name from the list of open windows at the bottom of the Window menu You can also select an Image window but not the Browser by clicking on its tab at the bottom of the Application window there is a tab corresponding to each open Image window Image demo63 sad Zooming and scrolling Image windows By default images are automatically resized so that they fit the Image window if you adjust the size of the Image window the image will be resized to fit it The procedures described later in this section show you how to zoom an image to produce magnified views However you can switch back to autosizing
193. with a non chemiluminescence sample in MultiGenius or ChemiGenius Alternatively you can choose a different configuration or change the settings or options manually before carrying out Step 4 2 8 Biolmaging Systems User Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Capturing an image yoo 4 Press the Image series button in the Image Capture toolbox to display the Series Capture dialog box Number of images in series 5 IV Add contents of previous images to each new image IV Use same exposure for all images in series Exposure control Exposure time E 01m 00s 000ms ll 5 Set the number of images you want to capture in the series by clicking on the arrow buttons next to the Number of images in series spin box you can choose from 1 to 100 inclusive 6 Check Add contents of previous images to each new image if you want the results to be cumulative each new image is the result of adding the new exposure to the previous image in the series Uncheck Add contents of previous images to each new image if you want all images in the series captured with the set exposure 7 Check Use same exposure for all images in series if you want to set a single exposure for all images Note If you check both Use same exposure for all images in series and Add contents of previous images to each new image the exposure time for the first image w
194. with your free hand before bringing the board into contact with the PC Biolmaging Systems User Manual Appendix 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Appendix PC Board and Software Installation To install a PC board 1 2 Disconnect the power lead from the PC Remove the outer case from the PC Remove the blanking plate from the PCI slot that you want to use for the board keep the screw for Step 5 Carefully fit the board into the slot you will need to push firmly but take care not to bend or flex the board or the PC s motherboard excessively Ensure that the lug on the bottom edge of the end plate is engaged and the edge connecter is fully inserted in the PCI socket Fix the end plate of the board to the PC s case using the screw from Step 3 Replace the PC s case Installing GeneSnap To install GeneSnap 1 Place the GeneSnap installation CD ROM in the PC s CD ROM drive The installation program should start automatically If it does go straight to Step 4 Otherwise If the program has not started within ten seconds and the activity light on the CD ROM drive is not illuminated follow Steps 2 4 Press the Start button in the Windows Task bar to display the Start menu and choose Run to display the Run dialog box Enter d setup and press OK to start the Grabber Support installation program or the equivalent if yo
195. ww artisantg com Getting Started with GeneWizard Press Open drawer button to release the drawer and then open it by pulling it towards you see note above Note If you have purchased the optional white light converter drawer and you want to capture an image using transmitted white light make sure it is fitted in place of the normal drawer 3 Place the sample in the drawer and push it closed until it is latched by the magnetic catch The buttons in the Image Capture toolbox will become enabled If you want the wells to appear at the top of the image place the gel in the drawer with the well line on the left hand side It is not essential to have the wells at the top of the image since GeneTools will analyze gels in any orientation However gel images are normally shown with this orientation so it is usually convenient to maintain this convention 4 Choose the Gel sample Configuration from the drop down list box in the Configuration bar at the top of the GeneSnap window Gel sample y Note This is one of the System default configurations supplied with GeneSnap see Working with Configurations page 5 1 to learn more about using Configurations The system is now ready to capture an image using one of the techniques in the following sections Capturing an image using automatic exposure To carry out an image capture using an automatic exposure 1 Follow the procedure in Inserting the sample see page 4 3
196. ystems are supplied with GeneWizard Darkroom fitted with 8 bit 16 bit performance provided by EDR CCD camera and prefocused f1 2 lens with standard UV filter Integral transilluminator 15 x 15cm 302nm sample size 15 x 12cm UV white light converter for white light applications optional Built in PC running Windows 98 Windows 2000 optional 250MB internal zip and 1 44MB floppy drive GeneSnap acquisition software GeneTools match analysis software Microsoft Office Small Business Edition optional GeneWizard is supplied with all necessary software installed in the PC so all you need to do is to connect a keyboard mouse and monitor Biolmaging Systems User Manual 1 17 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Introduction and Initial Setup Connecting up the System To connect up GeneWizard 1 Unscrew the knurled fixing screw holding the cover plate on the left hand side of the GeneWizard 2 Remove the cover plate to reveal the connectors beneath 3 Plug in the monitor keyboard and mouse leads the sockets are labelled with appropriate icons Note You should also connect any other accessories such as a printer to the appropriate connectors beneath the cover panel 4 Refit the cover panel slotting the cables through the cutouts and replace the knurled fixing screw to hold it in place 5 Connect power cables to the power socket
197. ze Go live button in the Image Capture toolbox to display a live image in an Image window Provided the drawer is closed the lighting control will show that the UV illumination has come on Transilluminator If No Light is selected in the lighting control select Transilluminator to turn the UV illumination on 3 To set the exposure time a Click in the exposure time control in the Image Capture toolbox to select the hours minutes seconds or milliseconds section of the box 00m Es 000ms Biolmaging Systems User Manual 4 5 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Getting Started with GeneWizard b Type the new value over the numbers or click on the up or down spin arrow at the left hand end of the control to increase or decrease the number 00m Ejs 000ms Note You can also increase or decrease the exposure time by pressing the up or down arrow keys on the keyboard or if you are using a wheel mouse by turning the wheel c If required select another section hours minutes seconds or milliseconds and edit that number you can click on the scroll bars at the right hand end of the control to move the selection to the next section E 00m 04s Mims IN As you increase or decrease the exposure time the live image will become lighter or darker adjust the exposure time to get a reasonably bright image of the gel without saturating any

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