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1. 20 colony forming ASSAY 48 COMED 27 33 16 UE SUME 14 Display Stati ni 31 Dual 26 Enhance IMAGES at 15 Export Image Sequence 32 F FOCUS 17 pm 15 Ciro 18 CH 14 H Histogram lt 31 dada adt dank Vd diia 37 I Image Another 20 OPERATOR MANUAL Image Microplate 14 ADO cR 16 L L veling M 6 RESINS 21 M Main Navigation Screen 10 Mean Loci Area 30 Menu ODEIOPIS nudo ct adidas 11 MEDIE Al 30 Minimum 30 N NEXU ROREM 16 Partial 15 Plate Carrier 6 Power Up Procedure 9 R 9 19 REMOVE
2. 17 19 E E 19 em 19 20 E 20 Review RESUS 21 Molecular Devices gt 2 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL 21 psa 25 LTEM 38 Batch Microplate 46 acre p 4 6 How tO Image USINO BSCUDS 46 Plate sities 47 EIGCe Place Cart Del E E E 4 7 Data Analysis ExamplesS centia SERERE RR RAD 49 Monoclonality o XU NOR CR CN X RR UR 49 Colony Forming Assay WOFKTIONM usi acia ac RC EGG 52 Health 55 Transport and 5
3. ies 55 ire IT TILES 55 E COVOIS 55 Si fers ag ers See ere ere Perey Terre rr er eer Cerne rire rer 55 55 Noise LOVGIS o A RR RE RR OR OR HC d 55 1 56 Cleaning CloneSelect IMAGES 56 Regular Maite aS 56 pip C 56 llli m 56 56 General a EQUUM DINER 56 Technical Specifications NN SENSE DIMENSIONS 57 EnvIFODnImeltELsusseadaxiadr RR RR 57 3 P o eme 57 SYMIPOIS on Gi 57 capes 58 Compatubie Plate
4. Molecular Devices gt 50 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL gt Now by clicking through each well in the Well Data list the well image will appear and monoclonality can be determined by looking back through the series of well images and identifying if the colony originated from a single cell Loci Count Plate Thumbnails Growth Rate Summary oris 2 Data 21 210 10 000 1 06 1 08 Area ym hes count m gt If the colony did originate from a single cell the well can be selected by either ticking the box or clicking the Yes button The well name can also be changed to reflect the clone if required Once all the wells have A7 been checked the list of selected wells containing a A10 monoclonal colony can be saved and printed for B3 further use pA Molecular Devices gt 51 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Colony Forming Assay Workflow Analyzing colony forming assay data sets are very similar to gating monoclonality data however the data export can be more detailed gt After imaging the plate of interest open the data point in Review Results The software automatically opens the data in the first tab Confluence gt Select the Thumbnails tab to display all the imaged wells Exclude any wells that have not formed colonies See the Plate Thumbnails tab section on how to exclude we
5. This is achieved in the following ways gt Right mouse clicking the Copy to Clipboard well of interest will display an Exclude selected from Process options menu where a single or MNT all wells and be excluded or Include selected in Process included Excluded wells are Exclude all from Process displayed with a red outline Included wells are displayed with a green outline Include all in Process gt Clicking the Control key the keyboard and the left mouse button will allows several wells to be selected These will be highlighted in yellow and the above menu will enable them to be included or excluded from the data set THUMBNAIL SIZE This slider enables the size of the thumbnails to be increased or decreased Molecular Devices 34 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Growth Rate Tab If a microplate has been imaged previously growth curves are displayed for all the wells in the plate The system determines if the plate has been imaged by looking up its barcode in the stored results so barcoded microplates should be used to enable this function Named plates can also be used but the name must be typed in exactly the same each time the plate is imaged for the software to identify the series The ability to rename plates also enables mis named plates to be included in the growth curve data if required Hovering the mouse over each data point displays the well co or
6. 2 a gt Within the exported results produced summary of the experiment criteria is displayed in the first rows the spreadsheet top left Molecular Devices gt 53 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL When the Colony area distribution is selected the following information is produced for each well Name if changed within the software Well number eg A1 Loci Count this is the total Mean Loci Area Bins equally splitting the loci area range into equal groups so that each identified loci will fall into one of the corresponding groups based on its size For example out of the 129 identified loci within well 1 119 of these fall into the first bin with a loci area range of 5589um to 58498 When selecting the Colony area and compactness for all colonies the area and compactness of each identified loci is displayed 2 Microsoft Excel Colony Forming Assay Results csv 3 59 60 Well ID 78 79 Q0 A4 oan C Cn wN Area 266 7923 173 415 266 7923 133 3961 173 415 320 1507 120 0565 6149 562 36510 52 653 641 106 7169 2281 074 813 7164 80 03767 93 37729 66 69807 493 5657 226 7734 106 7169 66 69807 46862 06 cc cnon7 4 4 Colony Forming Assay Results Ready Sum 27436 Compactness o x 191 File Edit View Insert Format Tools Data Window
7. gt Click Process to produce the loci counts for the selected wells The Loci Count tab screen will change to display an overview of all the selected wells and their corresponding loci count Confluence View Image Cell Number Loci Count Plate Thumbnails Growth Rate Summary Whole Plate Data 447 0 1 100 10 000 1 06 1 08 Loci Area ym Minimum Compactness 100 N N um P DER aaa 3 P 0 5 D 25 5 75 100 Loci Compactness Em X je See n X 3 6 wm m o X amp E i gt Click on one of the wells to display the well image The image will show the loci processing Molecular Devices gt 49 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Criteria Well E2 Data Area 1 Loci count ox 83 m 100 10 1 06 1 08 Loci Area um 5 O 16 8 4 0 Retum To Plate View gt Move the Minimum Area and Minimum Compactness lower and uppers sliders on the graphs to gate out any unwanted debris and misshaped colonies within the wells gt Click on Return To Plate View and check through some of the other wells to make sure all debris and misshapen colonies are excluded The plate overview will reflect the processing and display the new loci count number in each of the wells Criteria Whole Plate Data 0200064 0 IO
8. 20 Pee enV 23 Return To Plate 46 Review TOC US 15 Review FOCUS 16 S Save process as template 20 Save 20 Cole BAW 18 Scan Options 16 CY DS e 15 SBIGcE 16 Show enn mmn 26 re NITORE ETE TT ETT TERNER 15 14 W Woll Dalda 30 Well Name eenn mH Hmmm RH 27 lt 9 i i 8 Molecular Devices gt 68 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Contact Details Molecular Devices Queensway New Milton Hampshire BH25 5NN UK Tel 44 0 1425 624 600 Fax 44 0 1425 624 700 Web www moleculardevices com genetix For all technical queries please contact your nearest Customer Support group Visit www moleculardevices com genetix for latest contact details Trademarks ClonePix CloneSelect CellReporter Ha fBD NRich SlidePath Data Arena Image Arena are trademarks of Molecular Devices New Milton Ltd Copyright 2011 by Molecular Devices New Milton Ltd All rights reserved No part of this publication may be reproduced stored in a retrieval system or transmitted in any form by any means electronic mechanical by photocopying rec
9. x Molecular Devices gt 54 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Health and Safety Transport and Storage CloneSelect Imager must be stored and transported in temperatures within the range 25 to 55 C Lifting Points CloneSelect Imager is intended for bench top operation Care should be taken when moving CloneSelect Imager It is recommended that 2 people lift it External Covers Warning If any of the external covers CloneSelect Imager are removed the power supply is not automatically interrupted If it is necessary to remove any of the external covers you must ensure that the power is switched off first and do not attempt to use the robot until the covers are replaced Electrical Safety CloneSelect Imager must be connected to a properly earthed power outlet to protect users from the risk of electric shock The main chassis of the machine 15 earthed together with all associated electrical components Do not remove any of the fixed covers as there are no user serviceable parts inside All internal work should be referred to Molecular Devices approved service personnel Drive Safety There is a potential pinch hazard with the drive mechanism Please ensure that you do not attempt to load the plate until the drive has fully extended Noise Levels During normal operation the level of airborne noise emitted by the system will not exceed 7095 measured at 1
10. 58 ADDendIX DU 59 Well List File En bx ER Eaux Ra RE ERE REF EE EFE ERR FERRE MAE 59 RU MR e 00 Setting up Cell Number Estimation 60 Seno up a dilution T T TED TET 60 Molecular Devices gt 3 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Creating a cell number estimation TOFTRRU 61 Append REGHUESUNG a EICenSe Te 63 Ii ell ECONS Pme 66 12 2 2o een tere ee dudas xe UR NE EM EMEN OO Contact OO Molecular Devices gt 4 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Introduction CloneSelect Imager CloneSelect Imager is an automated CCD camera based system for imaging and confluence determination of cells growing in microplates Note CloneSelect Imager is strictly for research use only and is not intended or recommended for the diagnosis of disease in humans or animals If the instrument is used in a manner not specified in this manual the protection provided by the equipment may be impaired For correct functioning of the system users
11. gt Clicking on a frame will prompt the system to OOO0O000000000 capture and display a real time image Molecular Devices 46 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL gt The brightness and focus of the image can be altered at this stage Grab must be selected to set any changes made You are viewing well of a Genetix 96 well 1500 Brightness I 100 2 111 High Resolution Help Use the controls above to adjust the brightness and focus Click the Grab button to refresh the image Click the Next button to return to the well select screen gt The high resolution box can be selected to toggle between the high resolution 1 85 um and standard resolution 3 7 imaging modes gt If required the image can be exported as a bmp jpg or png file using the Export button gt To select another image or well go back to the plate view screen by clicking the back button gt To exit click the Next button on the plate view screen This will eject the plate for it to be removed and the process is finished Click Finish to exit the entire process and return to the E Scope process start page Plate Alignment This process enables the alignment of the plate within the system This process is carried out in the same manner as Alignment within the Image Microplate process but as a stand alone process and no subsequent imaging Eject Plate Carrier The Eject Pl
12. Properties The view of the process window when a process s properties are being set and prior to starting the process Progress The view of the process window when a process is executing Administrate Properties Can be used to alter the way properties are displayed It is not recommended that users alter these properties Molecular Devices gt 11 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Tools Menu Configuration Provides access to the configuration settings for the instrument It is strongly recommended that only Molecular Devices staff alter these settings Hardware Model View Accesses the datum positions for the instrument It is strongly recommended that only Molecular Devices staff alter these settings Prepare Error Report A wizard will create a data file containing the configuration and recent log files to help Molecular Devices Support diagnose recent problems Help Menu About Displays the version numbers of the software modules Most of these have the same version number so if asked to provide the software version number give this number unless otherwise directed Online Support Opens a web browser on the Online Support web page This function only operates if the workstation has internet connection e g network CloneSelect Imager User Guide An electronic summary of this operator manual is available however this guide is the comprehensive overview of the CloneSele
13. Molecular Devices gt 15 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Select Source Wells selected to be imaged are shown in red those not selected for imaging are shown in light blue Left click on a well to select it and right click to deselect Groups of wells can be selected or deselected by clicking the appropriate button and dragging over the wells The microplate type to be imaged can be altered via the drop down list Select plate type and wells to image 96 well w1500 0 9 Y Ge C Y 9 Y Ye Help Lise the mouse to select the wells to image cte esele ells are shaded red cted wells are shaded light Select All Deselect All Select multiple wells by holding Scan Options ow tto n the left mouse button and i over the Scan Type Full Scan 2 Review Focus Start Time 13 46 06 Import Displays an Open File dialogue box for importing a file containing a list of wells to be imaged The format of the file is given in Appendix B Select All Selects all the wells to be imaged Deselect All Deselects all the wells Scan Options Scan Type There are two scan type options Full and Partial Scan A full scan images the whole well so for a 96 well plate the imager takes four images per well to capture to entire well A partial scan images the centre of the well only so for a 96 well plate the imager would take a single image The partial scan results in a faster scan o
14. The file will display the plate barcode run date operator and the selected wells IMAGE TOOLS Zoom The slider can be moved either left or right to zoom out or in respectively The lowest magnification of the image is 18x and the highest is 144x When the figure turns red the system is zooming digitally and which may cause some pixilation of the image When zoomed into an image the zoomed area will be displayed on the image thumbnail to the right Contrast The contrast of the image can be improved by moving the slider to the left or right Return To Plate View Clicking this button will return the screen to the plate view within the Loci Count Tab so other wells can be viewed Molecular Devices gt 33 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Thumbnail Tab This tab displays the entire plate and the wells that have been imaged as thumbnails The thumbnails display the confluence overlay of each of the imaged wells Plate Type Genetix 96 well Barcode 008638 Processing Type Cell Detection Method 1 13 09 2006 08 30 Confluence View Image Cell Number Loci Count Plate Thumbnails Growth Rate Summary 4 This tab allows wells to be included or excluded from analysis This allows the analysis to be focused only on wells of interest Any wells included or excluded from the Thumbnails tab will be updated in the Confluence Cell Number Loci Count and Growth Rate tabs as well
15. Expire i The license for this software will expire in 4 days Would you like to request a new license now gt Click Yes This brings up the following window License will expire in 4 days This software requires a license to run You must first generate a license request file and send this to a support enaineer who can then issue a new license to you Request a new license Generate a license request file that a support engineer can use to issue a new license Install a license file Install a new license file issued to you by a support engineer Software version 1 3 45 961 gt Select Request a new license and click Next Molecular Devices 63 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER Please provide the following details This will help our support engineer to Create a license for you Registered User Company Institute Instrument Serial Number optional Motes Comments These fields are required E773 gt Enter the relevant details Click Next Click the save button to store the license request into a file Take note of where you save the file to so that you can locate it later gt Save file to a location where it is can be attached to an e mail OPERATOR MANUAL Molecular Devices gt 64 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Save the request to a file Desktop 191 Sea
16. Loci Count the Mean Loci Area the overview The Clear Loci button allows the loci processing to be cleared A prompt will appear warning that all the current loci data will be lost if continuing Export will enable the lists of wells and the Data Export corresponding Loci Count to be exported as a iin csv or xml file The Data Export wizard will guide the process of exporting the Loci Count data Select the type of results that you want to include Confluence and Cell Number data can also be exported at this point See the relevant sections for this description of exporting these data sets Select Cell Number Formula N51 The Loci Count criteria are automatically a populated from the gated Minimum Area and E MN Minimum Compactness graphs UA TTE Histogram Bins This option is used if the Maximum Area 1000000002 um Compactness Colony area distribution box is selected This Histogram Bins 20i value sets the number of equi sized bins for exporting loci frequency counts The default value is set to 20 bins Colony area distribution Colony area and compactness for all colonies Previous Next gt Cancel Colony area distribution When this box is semine selected the colony area distribution data is divided into the number of bins specified in the Histogram Bins and displayed with any other exported data Note Only w
17. final time point in order to observe the migration taking place in the wells If time points are restricted by the End Time Point option in the Graph display of the Well Details tab animation will only occur using the time points available Molecular Devices 40 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Well Details Tab This tab provides all the details generated from individual wells There are two displays available within this tab Image Display and Graph Display IMAGE DISPLAY This display shows all the information gathered from the individual well images A whole well image is displayed center screen with time point thumbnails below Click on any of the thumbnails in the film strip to display the enlarged image for that time point The Display Graph header will change the view to the Graph view of the data Plate Type Greiner 96 well 781098 Barcode 007055 Processing Type Cell Detection Method 1 Overview Thumbnails Well Details Display Graph Imane Tools Contrast No Overlay Overlay Cell Growth 0 0000 mm 2 2403 mm 2 6967 mm Overlay Wound Well Information Well Name Total Migration Area 2 6967 mm Focus Position 1 331 Brightness 92 96 Image Tools Zoom Using the slide bar it is possible to zoom into any region of the well When zoomed into the image it is possible to click and drag to anywhere on the image A small zoom box will app
18. meter Molecular Devices gt 55 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Maintenance Cleaning CloneSelect Imager The machine should be cleaned each day Clean the machine using 80 ethanol or dilute detergent and a lint free cloth Organic solvents and abrasive cleaners should not be used as they will damage the cover Do not pour cleaning solution directly on to the machine or other objects apply using a Suitable lint free cloth Regular Maintenance Daily gt Ensure that CloneSelect Imager is free from dirt and dust see Cleaning CloneSelect Imager above Weekly gt Check operation of equipment Check calibration gt Check for damage Annually gt Maintenance by manufacturer We would strongly recommend that maintenance be carried out regularly and by a Molecular Devices approved service engineer Maintenance contracts can be obtained from Molecular Devices see Contact Details on page 69 General Precautions gt All waste must be disposed of according to local regulation gt Do not use in explosive environments Molecular Devices 56 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Technical Specifications Manufactured by Molecular Devices New Milton Ltd Dimensions Total assembled Size height Weight 575mm width x 720mm depth x 438mm Excluding ancillary equipment 45 kg Operating Environment Indoor use only Tem
19. there 15 more than one copy of the same data set present in Duplicate results are present in this results location Please select the Image Archive folder the following error message will be 49 subfolder in the results location that does not contain duplicates displayed when trying to open the data set The duplicated data should be removed from the Image Archive folder If results have been deleted from the Image Archive folder the data set will still appear in the Review Results list If this data set is selected the following error m essa g e wi a p pea 9 The selected results are invalid Invalid Results Delete the data set from the Review Results screen to completly remove Molecular Devices gt 21 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Manage Results VIEW RESULTS View results To view results either double click on the data of interest or click to Export results highlight the data and then click View Archive results Multiple data sets can be selected by holding down the Shift or Control keys while clicking the data of interest to select contiguous or non contiguous sets of data respectively EXPORT Displays a wizard that allows data from the selected results to be exported A variety of formats are available Reprocess results Delete Rename ARCHIVE The results for runs stored in the default location C Image Archive can be
20. 00 1 06 1 08 Loci Area Minimum Compactness 0 In the Loci Count tab the plate view displays each well with a figure indicating the number of cell colonies found in the well The default plate view displays the Loci Count Under Display Statistic however this can be changed to Mean Loci Area which will display this value within each of the wells To display the Well View for a well click on the desired well in Plate View or in the Well Data list CRITERIA Minimum Area The loci count frequency is plotted against the loci area um in a log scale The bar chart has two lower and upper gates that can be moved accordingly to eliminate unwanted objects debris within the well that artificially inflate the number of loci Minimum Compactness The loci count frequency is plotted against the loci compactness The bar chart has two lower and upper gates that can be moved accordingly to eliminate irregularly shaped objects from the loci count Compactness is the relation between the area and the perimeter expressed as a ratio of the actual area and that of a perfect circle with the same perimeter WELL DATA This lists the wells The well name can be changed if required by clicking twice on the well name and typing in the desired name Name Molecular Devices 30 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL DISPLAY STATISTIC The drop down menu will display either the
21. 07 67 66 69 9 09 1 2 9 3 0 is option will print a schematic 8 69 55 65 5 02 62 9 2 5 6 6 resentation of the confluence overview 9 plate format The confluence 29 0309 03 09 25 09 04 50 03 54 09 values are displayed within the wells 0 0000000000000 05 09 069 00 and the plate details are displayed at 09 59 59 89 089 04 59 09 9 0X 04 09 the top of the overview Export This will enable the list of wells and the corresponding confluence to be exported date Export as a csv or xml file The Data Export A paoman wizard will guide the process of exporting the confluence data Cell Number and Loci Count data can also be Select the type of results that you want to include exported at this point See the relevant sections for the description of exporting EN these data sets Select Cell Number Formula The wizard provides the option to export the data for the following time points Loci Count May require time to generate data Select which time points ta export J The curently selected time The most recent time for each well plate amp The complete time series lt Previous 4 gt Cancel By default the Annotation text box displays the number of wells that have been imaged This can be edited to more meaningful annotation Note This can not be changed when viewing the data through a remote data viewer Molec
22. Mol Qoevices CloneSelect Imager OPERATOR MANUAL SOFTWARE RELEASE 1 3 73 1073 Control 05MAN1070 A5 Effective Date xx xx xx ECO 3092 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Contents 1 eases saan a a ager id sa eae 5 asl 5 5 Hardware a Layoust ang 6 P Errem TET 6 8 calpration ung A A a a 9 Foner Up a Aaa 9 Starting up CloneSelect Imager LO CloneSelect Imager SOMWale aaa 10 Menu a S OE RR 11 ET EA ET T T AET E ET A E PET T EEEE E E NIE A 11 12 12 Main Navigation a 13 13 EET 13 aice pndauig e 13 D E STENT 13 CloneSelect Imager Processes eeeeee eene nenne 14 MICFODISEB cers 14 Imaging Ferna oeU Roo et re eee err 14 2121 28 16 17
23. Number Formula Loci Count May require time to generate data Molecular Devices gt 29 of 69 Enter the cell number for some or all wells in to the grid on the left Click the Generate button to create a line of best fit To adjust the line click and drag the purple and orange squares To save the estimation enter a name for the formula and then click the Save button You can quit at any time by clicking the Discard button Discard Save lt Previous Next gt Cancel MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Loci Count Tab Generated images can be processed using the loci count feature This detects and counts the number of loci of growth i e cell colonies for applications including monoclonality verification and colony forming assays If a plate is imaged multiple times during colony growth the history of each well with one identified colony can be viewed for visual proof that the colony is derived from a single cell progenitor For colony formation assays the Loci Count feature can be used to count the number and size area of colonies in each well Plate Type BD Falcon 96 35 3072 Barcode CHO LD 10 1 09 P2 Processing Type Typical Adherent Cell Confluence Confluence View Image Number Loci Count Plate Thumbnails Growth Rate Summary 1 2 3 4 9 6 7 8 9 z el 12 Loci count M wx c 100 10 0
24. ages of your microplate Maintenance Processes Plate Alignment Eject Plate Carrier By Adjust the alignment of a plate in the system ta Ejects the plate carrier for maintenance cleaning the glass etc Utility Processes Result Location Administrator Process to allow the management of result locations Open Process CloneSelect Imager Software CloneSelect Imager software is based around the concept of the instrument running processes The instrument has a default set of processes that can be modified and saved Processes are managed from the Main Navigation Screen which is the view displayed when the software starts Molecular Devices 10 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Menu Options The same menu is displayed in all the windows but some item availability may vary between windows File Menu Open Process Allows previously saved processes to be opened Save Process Saves the current process Save Process As Allows the current process to be saved with a different name or location Close Process Closes the current process and re opens the Main Navigation Screen Save As Template Saves the current process as a template Recent Processes Allows a recent process to be selected and opened Switch User Allows a user to log off and another user to sign on when User Authorization is licensed within the software Exit Exits CloneSelect Imager software View Menu
25. archived to CD DVD or the network disk Click Archive results to open the Archive window Note Archive results is not available for results that are not stored in the default location To move such results to other locations or burn to CD DVD use Windows Explorer Note Archive to CD DVD is only available with Windows XP Archive to CD DVD Select CD DVD as the archive type Hel Select an archive type 5 CD DVD Network Disk Ar Am ing to Network Disk ct the locatio 2 which the data sno Archive to CD or DVD be archived by clicking the Browse ns viis data from pi loc 2 ali Archive Name it has tes pied to the new loc che ck 7 the tick bot Media Type DVDS 4 7GB DVD R R Cick the Archive button to begin archiving ids Delet It i itten elete result images once written tke archive Sele 2 media type CD A for a writable CD CD BWfor a se witable CD DVDS for a single layer writable DVD DVDS for a dual layer writable DVD To remove the stored image data E v the amd uter v when the disk has bee check the tick box Click the Archive button to begin archiving Archive Name Give the archive an appropriate name Media Type Select the media type from the drop down list An explanation of the media types is given at the right hand side of the screen Delete result images once written If checked the result files are deleted from the C Image Archi
26. ate Best Fit Clicking on this will automatically generate the line of best fit if required Molecular Devices 28 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER Create New OPERATOR MANUAL Clicking this will enable a new cell number estimation formula to be created Ensure that the confluence results displayed in the Confluence Tab are those for a standard plate containing known numbers of cells The software will automatically select up to twelve wells with confluence values ranging between 10 and 80 and display them at the bottom of the graph The name for the new formula should be entered in the top right hand corner and the cell numbers for each well should be entered into the corresponding well number box to the left of the graph Clicking Create after all relevant information is entered will create the new formula WELL CELL NUMBER A list of estimated cell numbers is displayed to the right of the plate overview Export will enable the lists of wells and the corresponding Cell Number to be exported as a csv or xml file The Data Export wizard will guide the process of exporting the Cell Number data Confluence and Loci Count data can also be exported at this point See the relevant sections for this description of exporting these data sets Please enter some or all of the cell numbers for the wells below Data Export Select the type of results that you want to include Select Cell
27. ate Carrier process provides a means of ejecting the plate carrier for cleaning or removing a plate if it has been left in the instrument Clicking Start will eject the plate holder Clicking Next will return the plate carrier into the instrument Click Cancel to exit the process and return to the starting page of the Eject Plate Carrier process Molecular Devices 47 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Click Finish to return to the starting page of the Eject Plate Carrier process Molecular Devices gt 48 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Data Analysis Examples Here are some examples of how to use the features of the CloneSelect Imager software to analyze various data sets Monoclonality Workflow gt After imaging the plate of interest at several time points open the latest data point in Review Results The software automatically opens the data in the first tab Confluence Confluence View Image Cell Number Loci Count Plate Thumbnails Growth Rate Summary gt Select the Thumbnails tab to display RR all the imaged wells Exclude any wells that do not appear to have 1 colony within the well See the Plate Thumbnails tab section on how to exclude wells gt This will save time by not processing wells that do not contain 1 colony gt Open the Loci Count tab The well diameter can be adjusted if required
28. ate map shows all of the wells that were imaged and are plotted on the graph Any wells that are not imaged will be grayed out Any wells can be included or excluded from this data by clicking on the Select All or Select buttons Wells can selected deselected using the left and right mouse buttons respectively When wells are selected they are displayed in yellow When wells are deselected they are displayed in blue This feature enables the selection of wells to plot on the graph This selection deselection of wells only applies to the graph and not the overview Select Comparison Wells Select Comparison Wells Left click and drag to select wells Right click and drag to deselect wells Left click and drag to select wells Right click and drag to deselect wells 1 2 3 4 5 6 7 8 9 10 11 12 1 2 3 4 5 6 7 8 5 10 11 12 180000 BODO 100000000000 1200000 000000000000 180006 6660000000000 0000090090000 Select All Clear All OK Select All Clear All OK End Time Point This drop down menu lists the time points of the imaged plate It is possible to select the desired end time point directly from the menu or by scrolling through the time points using the arrows When the end time point is selected the graph will display only the time points prior to and including the end point selected Plate Type Greiner 96 well 781098 Barcode 007055 Processing Type Cell Detection Method 1 Overview Thumbnails Well Details Dis
29. ces gt 38 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL exported as a CSV Excel XML or XML file Molecular Devices gt 39 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Thumbnails Tab This tab provides an overview of each well image and the scratch wound detection The thumbnails can be copied to the clipboard by right clicking anywhere on the thumbnail map Plate Type Greiner 96 well 781098 Barcode 007055 Processing Type Cell Detection Method 1 Overview Thumbnails Well Details Time Points qe Start Animation LP 4 zd a me 8 1 i i i af T sts pe P 4 28 E E al ad m negro dri f 4 lb Zoom Sliding the bar will enlarge reduce the entire thumbnail map allowing navigation to any well of interest It is possible to click and drag on the thumbnail map to scroll to the well of interest Time points The drop down menu lists all of the time points the plate has been imaged A time point can be selected from the drop down menu or by clicking on the arrows to the side of the menu If the time points available are restricted by the End Time Point in the Graph display of the Well Details tab only the selected time points will be displayed here Start Animation Clicking this button will animate the thumbnails from the starting time point to the
30. ct Imager software Molecular Devices gt 12 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Main Navigation Screen The main screen enables navigation of CloneSelect Imager imaging and maintenance processes New Process Tab The New Process tab provides CloneSelect Imager Processes for imaging microplates or reviewing results It also contains Maintenance Processes for various setup features of the system CloneSelect Imager Processes Image Microplate Standard imaging of microplates Review Results Review of results from previous runs including confluence cell number estimation and monoclonality analysis Batch Microplate Imaging Imaging of batches of plates with the same configuration E Scope High resolution imaging of microplates Maintenance Processes Plate Alignment Allows the alignment of a plate to be adjusted in the system Eject Plate Carrier Ejects the plate carrier for cleaning and removal of microplates Utility Processes Results Location Administrator Allows the management of the results locations Templates Tab Saved templates can be retrieved by clicking on this tab Template files can be saved as files using the Save process as template option found in Image Microplate Recent Processes Tab Recent processes can be retrieved by clicking on this tab Recent processes can be saved as gfp files using the Save process option found in Image Microplate Open P
31. d Time Point option in the Graph display of the Well Details tab animation will only occur using the time points available GRAPH DISPLAY This display shows the information gathered from the individual wells and displays in graph format The graph is displayed center screen with Migration Area mm plotted against Time hours A time point thumbnails of the selected well denoted by a red line on the graph is displayed below the graph Plate Type Greiner 96 well 781098 Barcode 007055 Processing Type Cell Detection Method 1 Overview Thumbnails Well Details Display Images Wells Selected Well 7 Plotted Wells T E E c lt o m Time hr Select All Select 0 0000 mm 2 2403 mm 2 5498 mm 2 6967 mm Fnd Time Point 722hrs ud 24 1 hrs 48 0 hrs Each thumbnail image in the film strip displays the total migration at that time point and time passed since the first time point in the series When hovering over a data point on the graph for the selected well denoted by a red line on the graph the corresponding thumbnail will be highlighted in red The Display Images header will change the view to the Images view of the data Molecular Devices 43 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Wells Selected Well This is the well currently selected and displayed on the graph as a bold red line Plotted Wells This pl
32. dinate for that point Plate Type Genetix 96 well Barcode 008638 Processing Type Cell Detection Method 1 11 09 2006 14 19 x Confluence Image Number Loci Count Plate Thumbnails Growth Rate Summ immary Display Mode 9 Data Points Averages Select Well Include Timepoints v 15 09 2006 08 36 Z 14 09 2006 08 17 1 13 09 2006 08 30 1 12 09 2006 08 48 1 11 09 2006 14 19 Confluence 96 Growth Rates Well Total Growth Mean Rate A1 39 0 0 432 39 0 0 432 eh tn e 430 0476 Ob d E A7 390 0432 5 Bos Y BU si gt ea 410 0 454 beo het 36 A ori G von te 6 39 0 0432 du gt Aat We def A D Sg d uo e 1 days 18 2 days 17 58 hrs Pint Export Close DISPLAY MODE The growth rate graph can be displayed with all the well data points by clicking the Data Points option or as averages by clicking the Averages option 53 J 2 The thick red line within both graphs is displaying the growth rate for the selected well e g Al The well z schematic below the graph is also displaying the captured images for the selected well 44 55 Time Hours SELECT WELL This drop down menu allows the well to be changed INCLUDE TIMEPOINTS This box allows various time points to be incl
33. e automatically populated using the Minimum and ane 51 Maximum Area and Minimum and Maximum Compactness data set in the Loci Count Tab 14 Plate Thumbnails Loci Count Clicking Generate will require the report to be saved as a html file before it is generated Loci Criteria Well Diameter mm Minimum Area 5 um Minimum Compactness T Maximum Area um Maximum Compactness 100 EXIT To exit Review Results click Cancel which will display the list of data in Review Results Click Cancel again to exit this page click Finish to close the process entirely and return to the Main Navigation Screen by clicking Close Process Molecular Devices 37 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Migration Application Migration analysis is carried out on data that has been imaged over a number of time points For each data set analyzed the Plate Type Barcode and Processing Type is displayed at the top of the screen Overview Tab This tab provides an overview of the migration assay data A heat map is generated and can be displayed using one of three parameters Migration Rate This is a measure of the rate of increase in cell movement mm per hour over the entire time period Total Migration This is a measure of the increase in area of cell movement mm over the entire time period Maximum Migration Rate This is a measure of the largest rate of increase in cell mo
34. e file Install a new license file issued to you by a support engineer Software version 1 3 45 961 gt Click Next Click the Open button and locate the license file sent to you by a support gt Click Open and browse to the location where the license License file was saved gt Open the file Molecular Devices gt 66 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL gt A window should appear to indicate that the license file was successfully installed The new license was successully installed Your new license file has been successfully installed You can now continue to use this application Press Finish to continue gt Click Finish The software will now start If for any reason the license does not appear to work as expected please contact Customer Support for assistance Molecular Devices 67 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER Index A 9 26 22 Auto focus before run 15 Averages 35 nena 15 9 C 16 Cell Detection Method 1 15 Cell Detection Method 2 15 Cell Detection Method 3 15 Close 5
35. ear on the navigation panel to identify the image region being viewed Contrast It is possible to increase and decrease the contrast of the image using the slide bar if required for better visualization of the cells No Overlay When selected no detection of any part of the image cells or wound is displayed Overlay Cell Growth When selected only the detection of the region of cells is displayed in green Overlay Wound When selected only detection of the regions without cells is displayed in green Molecular Devices 41 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Molecular Devices gt 42 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Well Information Well Name The displayed well can be selected from the drop down menu or by using the arrows to scroll through wells Total Migration Area This value is a measure of the total cell growth in mm over the entire time period for the selected well Focus Position This is the focus position used for the microplate Brightness This is the brightness value used for imaging Export Image It is possible to export the well image as a bmp jpeg or a png Start Animation If this option is selected each of the images in the time point series will be displayed as an animation to aid visualization of the migration of cells The animation will always start from the first time point in the series If time points are restricted by the En
36. eed to autofocus on every well Leveling Feet The leveling feet can be adjusted by loosening the locking nuts and turning the feet until the instrument is level and stable Retighten the locking nuts once any adjustments have been made Molecular Devices gt 6 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL The overall layout of the instrument Top View 428 Side View Front View Note All dimensions are in millimetres Molecular Devices gt 7 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Setup Locating CloneSelect Imager CloneSelect Imager should be situated on a stable level surface Level the instrument by loosening the locking nuts and turning the leveling feet to ensure that it is stable and not able to move Retighten the locking nuts after adjustment Workstation CloneSelect Imager is supplied with a Dell T3500 Workstation with special hardware and software to support the imaging function Do not attempt to use any other workstation to operate CloneSelect Imager The workstation is supplied with Microsoft Windows 7 and will require security configuration if it is to be connected to a network If that is done ensure that no changes are made to the configuration of the private network connection to the CloneSelect Imager since that will stop it operating Microsoft Office with standard English settings The performance of the system may be affected if these setti
37. ell the Grab button must be clicked to display the newly selected well Grab This Grab button must be clicked after altering any settings to retake the image Save Image Clicking on Save Image will display a Save File dialogue that will allow the current image used for focusing to be saved Images can be saved in bmp jpg or png format Processing Type This drop down menu displays the three Cell Detection Methods to choose from See page 15 for the description of the three Cell Detection Methods Generate Confluence Selecting this box will identify and highlight in green all objects within the well Scale Bar A scale bar is displayed in the lower left of the window This resizes automatically as the zoom level is altered Molecular Devices gt 18 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Alignment The Alignment window ensures the camera is properly aligned with the wells of the microplate Four images are taken over the north south east and west edges of well 1 The well edges should line up with the four red lines If they do not line up clicking and dragging the lines will correct the alignment to view the new alignment or Next to continue Re image This button should be clicked if the Re image button is highlighted in pink This will recheck the alignment following adjustment Brightness Level The brightness level of this image can be altered by movin
38. ells included selected in the Well Data list are exported Colony area and compactness for all colonies When this is selected a list of all colonies in all wells is exported with the area and compactness for each colony Note There is no filtering so all the data is listed Molecular Devices gt 31 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL WELL VIEW Clicking on the well of interest in the plate view of the Loci Count Tab will display the image for the well with an overlay over areas of growth detected according to the Minimum Area and Minimum Compactness criteria Plate Type BD Falcon 96 35 3072 Barcode CHO LD 10 1 09 P2 Processing Type Typical Adherent Cell Confluence 15 10 2009 11 10 Criteria Well A7 Data Minimum Area Loci count gt 100 10 000 1 06 1 08 Loci Area 2 o o o If the microplate has been imaged at several time points film strip of schematics of the well at the various time points is displayed across the bottom of the screen with loci colored in green Click on any of the schematics to display the well image at that time point with the loci from the latest image outlined This provides a means of checking if a colony has resulted from a single cell or from more than one cell For an example of analyzing monoclonality data see the Data Analysis Examples section of this manual Plate Type BD Fa
39. etting up a dilution series Setting up a dilution series gt Check viability of your cell line e g using Trypan Blue It is essential that viability is high 95 100 gt Prepare a cell suspension in complete medium with the following density 1 000 000 106 cells ml for suspension cells e g hybridomas 250 000 cells ml for adherent cells gt Create a dilution series i Number of cells 2001 dilution Cell suspension Medium HI HI Suspension cells Adherent cells 100 2000 200 000 50 000 1500 500 150 000 37 500 gt Dispense 2001 aliquots of each dilution into 96 well plate plating out at least 4 replicates for each dilution It is recommended to dispense the cell samples vertically to ensure an even spread of cells gt Incubate the plate to allow the cells to settle For suspension cells it is recommended to leave for 30 minutes and for adherent cells leave at least 4 hours to attach Molecular Devices gt 60 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Creating a cell number estimation formula gt Image the dilution series on CloneSelect Imager gt In the Confluence tab check that the dilution points with confluence between 5 and 80 have acceptable replicates Plate Type Genetix 96 well W1500 Barcode Hybridoma Calibration Confluence View Image Cell Number Plate Thumbnails 5 6 5 4 3 2 1 0 0 25 50 Confluence Show Cumu
40. f all the wells to be imaged Review Focus By selecting this tick box the focus of the image will be reviewed before the scan begins Next Once the wells to be imaged have been selected click Next to move to the next stage This button is present throughout the entire process but may be grayed out where its use is not applicable Cancel Click Cancel to exit the process and return to the starting screen of the Image Microplate process The button is present throughout the entire process but may be grayed out where its Molecular Devices gt 16 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL use 1 not applicable Load Plate The plate carrier is ejected to enable the loading of the microplate Ensure that well Al is to the back right corner of the plate carrier Focus The Focus window allows the image to be optimized before the scan takes place Processing Type Cell Detection Method 1 Generate Confluence Help Use the controls above to adjust the brightness and focus Click the Grab button to refresh the image Click the Next button to Start Time 13 45 06 Brightness The software automatically determines the optimum brightness setting for imaging However the setting can be adjusted via the Brightness slider After adjusting the brightness the Grab button must be clicked to retake the image using the new settings Saturated pixels will be displayed in red so it is
41. facturer often supplies several plates of the same well format with different catalogue numbers In many cases these plates have the same dimensions so if your plate type does not appear in the above table contact Molecular Devices New Milton Ltd Molecular Devices gt 58 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Appendix B Well List File Format This appendix describes the format of a Well List file to be imported into an Image Microplate process via the Select Source window The file containing a list of wells to image should be a text file txt with the plate type as the first line Each well to be imaged is then entered on a new line Note that each file describes a Single plate only PetriWell 96 well 5 E8 etc Molecular Devices gt 59 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Appendix C Setting up Cell Number Estimation The confluence values measured by CloneSelect Imager can be used to non invasively estimate the number of cells in each well This is achieved by a cell number estimation formula Because of the variation in size or properties of different cell types e g adherent versus suspension cells it is essential to generate a cell number estimation formula for each cell type Generation of the formula on CloneSelect Imager requires preparation of a dilution series of your cell type with known cell number The following section provides guidelines for s
42. focus before run F Processing Type Cell Detection Method 1 Setup Review focus If enabled the Focus window is displayed before the microplate is imaged to allow the focus and brightness settings to be checked before imaging a microplate Individual images can also be saved from the Focus window Auto focus before run If enabled the instrument carries out an auto focus procedure before imaging the microplate Scan type Select Full Scan to image the entire area of each well in the microplate In Partial Scan an area from the centre of each well is imaged This speeds up imaging and is suitable when the data from the centre of each well is representative of the well as a whole Enhance Images Selecting this option will normalize flatten the background of the images to enhance them for display Processing Types The following processing types have been developed for cell and colony detection Cell Detection Method 1 Formally know as Typical Adherent Cell Confluence this algorithm is ideal for settled Suspension cells and adherent cells with good contrast Cell Detection Method 2 This algorithm helps to detect cell samples when contrast is low cells are clumped or at the edge of the well Cell Detection Method 3 This algorithm is designed to detect colonies and distinguish them from any artefacts around the edges of the colonies Start Once the process s properties have been set click Start to enter the process
43. g the slider Note This will only change the brightness for this alignment image Imaging Plate Type 96 well 1500 Barcode 003026 Processing Type Cell Detection Method 1 During the imaging run a schematic of Corer View Image the plate is displayed with the image frames superimposed in light blue As images are captured and processed the frame changes color to light brown then green _ E a 2 7 Nd 2 Ey ay EJ Once a frame has changed to green it is possible to click on it to display the image in the View Image tab Clicking on the Confluence tab will return the screen to the plate view Any unselected wells will not be imaged and are displayed as a blue square Start Time 13 46 06 Results The results of the Image Microplate process are displayed The images can be reviewed here or they can be viewed via Review Results once the process has finished completely Molecular Devices gt 19 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Remove Plate When Imaging is complete the microplate will be ejected from the system Within this screen there is the option to repeat the imaging with another plate or move onto the next step of ending the process Image Another Plate Another plate can be imaged using the same configuration This is achieved by clicking Image Another Plate instead of Next The plate carrier remains in the ejected position and the Select Source
44. he E Scope process provides a means of capturing higher Take single Hi res images of your microptite resolution images of cells 1 85 um without performing any image analysis Frames to be imaged can be freely selected 2 clicking with the mouse on the screen The setup of the E Scope process is the same as Image Microplate How to Image Using E Scope gt Select the microplate type to be imaged by clicking on the Source Header and selecting the appropriate plate from the drop down list Click Apply to set the changes gt Click Start to commence the process gt Load the plate making sure well A1 is placed to the back right corner of the plate carrier Click Next to load the plate Cancel can be clicked to exit the process at any point gt When prompted check that the camera is properly aligned with the wells of the microplate The brightness levels of the image can be changed if required by moving the slider Ensure the Re Image button is clicked if 123 4 S 6 7 8 9 1 mH 2 any changes are made to recheck the alignment Click Next once satisfied with the image and well COKCOICOICOICOICOICOICOICO alignment gt The system displays a schematic of the microplate Showing all the possible image frames COO ICICI CC IC IC
45. important not to make the image too bright Focus The system stores the last focus setting used for each plate type So after a plate type has been imaged for the first time the focus setting should not need to be altered significantly After altering the focus setting the Grab button must be clicked to retake the image using the new setting The altered focus setting now becomes the default focus setting for the plate type being used in this run Clicking the Auto Focus button will start the autofocus procedure This may take a minute or two If there is debris on the bottom of the plate or on the glass plate carrier the autofocus may focus on these instead of the cells If this is the case the focus will have to be adjusted manually Zoom The Zoom slider can be used to zoom into the image This can also be achieved by clicking on the image and using the mouse wheel to zoom into the image While the zoom setting Molecular Devices gt 17 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL figure e g x 99 displayed to the right of the slider is black the system is zooming optically When the figure turns red the system is zooming digitally and some pixilation of the image may be seen Change Well By default focusing is performed on well or the first well of the plate to be imaged if 15 not selected to be imaged Different wells can be selected to focus on from the drop down list After selecting the desired w
46. is 07 42 0 95 displayed as gt 80 Hovering over a well causes a tool tip to appear displaying the well co ordinate and the confluence for that well Clicking on a well will display the well image in the View Image tab Right clicking on the overview will allow the overview to be copied to clipboard Molecular Devices 25 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL CONFLUENCE DISTRIBUTION The bar chart at the top right of the window shows the number of wells with a given confluence level Dual Gates The arrows pointing down at the top of the bar chart can be dragged across the chart As both lower and upper arrows are dragged the corresponding confluence data is displayed Any wells that do not fall inside these lower and upper gates will be grayed out The text displayed below the chart will update to give the number of wells that fall within the selected confluence e g 10 out of 36 wells selected for analysis have a confluence of between xx and xx Show Cumulative When checked the individual bars in the chart will merge to show the confluence as continuous data Barcode Ed CHO Cell Count Test Date Imaged 14 June 2006 09 05 33 WELL CONFLUENCE The confluence for each well is displayed in the list to the right If desired the well name can be changed in this list by clicking twice lt on the well name of choice 68 68 57 65 87 56 40 23 2 7 3 2 VETERE
47. iving is being carried out to free space on the C Drive Archive Click Archive to send the results to the selected destination DELETE Deletes all the images and results for the selected data set RENAME Barcodes plate names can be re named in case of any misnamed plates which will subsequently be excluded from growth curve data This can be achieved by clicking on the barcode name to be changed and clicking Rename A small dialogue box will appear in place of the barcode name to enable a new barcode name to be typed in its place Results Selection RESULTS LOCATION If results have been saved to a different location not Image Archive it is possible to browse to another location using this feature Molecular Devices 23 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Other Applications MIGRATION This option does not appear if the software has not been licensed for this application To view the data for a migration assay click on the relevant data set and click on the Migration link to open the software application The migration data analysis screen will open and the data is displayed within three separate tabs Overview Thumbnails and Well Data When the data is opened the Thumbnails tab will be grayed out and display Loading This allows extra time for the images to be loaded into this data tab Meanwhile data can be viewed in the other tabs The Migration link is disabled and grayed out in the fo
48. k on Review Results to start the process Load Results The default location where imaging results are stored is the C Image Archive folder All the image and data files for each individual run are stored in a folder that is named with the date and time stamp for the run e g 2005 11 01T11 52 10 Within the Image Archive folder the run folders are automatically organized into separate folders for each month e g 2006 10 When opening the Review Results process on the CloneSelect Imager the user is directed straight to the results Plates imaged on the system are displayed as a list If free space on the disk is running low the bar at the top of the window appears orange and a warning is displayed in the top right corner If disk space is getting critically low the bar is colored red Load Results Manage Resuks Barcode Wellplate Operator Annotation Disk Space 3 View Archive 17 06 2011 13 53 28 006393 well Administrator 1 well has been imaged 8 06 MB ia Export 17 06 2011 13 50 37 003026 Well Administrator 60 wells have been imaged 423 59 MB 17 06 2011 09 31 55 003026 96 Well Administrator 12 wells have been imaged 84 45 MB 7 Archive Delete 27 Rename Results Selection 22 Results Location Runs Date Results Other Applications 1 Migration In Field All Showing 29 of 29 Start Time 13 55 21 Right click on a selected run to display the context menu Duplicate Results If
49. l Number Loci Count Plate Thumbnails Growth Rate and Summary This window opens with the Confluence tab displayed by default The Plate Type Barcode and Processing Type are all displayed above all the tabs to make it clear which data set is being viewed throughout the processing Confluence Tab This tab displays the confluence level for each well both graphically and as a list Plate Type Greiner 96 well Barcode Ed CHO Cell Count Test Processing Type Cell Detection Method 1 Yesterday 09 05 Confluence View Image Cell Number Loci Count Plate Thumbnails Summary Confluence Distribution 1 2 3 EH 100 m N ot wells n en wW e 25 50 75 Confluence 96 Show Cumulative 36 of 36 wells selected for analysis have a confluence of between 0 and 100 Well Confluence Name Well B1 B2 B3 B4 B5 B6 B7 B8 B9 B10 B11 B12 Annotation 36 wells adCHO calibration curve PLATE CONFLUENCE OVERVIEW Each well is represented by a pie chart of the confluence level for that well The pie charts are color coded such that low confluence is green and high confluence is red with shades in between representing the intermediate levels Hovering the mouse over the pie chart area causes the percentage confluence for all the wells to be displayed Confluence that is detected as 4 lower than 5 percent is displayed at lt 5 and confluence above 80 percent
50. lative 24 of 24 wells imaged have a confluence ol 0 or greater Annotation 24 wells have been imaged Confluence tab with expected dilution point confluence percentage gt In the Cell Number tab click on the Create New button Plate Type Genetix 96 well W1500 Barcode Hybridoma Calibration Confluence View Image Cell Number Plate Thumbnails 1 2 3 117 780 57440 104100 Cell Number tab Viewed with a previously defined cell number formula gt This opens the Cell Number Graphical Display window Molecular Devices 61 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL gt For wells with confluence between 5 and 80 input the cell number associated with the wells into the table in the left panel gt Click on the Generate button to create a graphical plot of the data and the statistical equation shown in the top left corner If data has been inputted incorrectly it can easily be re entered and corrected using the Generate button or all of the cell Formula Details lease enter some numbers for the wells below 0 944 Formula Name Well Number F 52 100000 150000 z 25000 5 28 50000 2 100000 24 150000 2 12500 2 25000 50000 2 100000 Enter the cell number for some all wells in to the grid on the left Click the Generate button to create a li
51. lcon 96 35 3072 Barcode CHO LD 10 1 09 P2 Processing Type Typical Adherent Cell Confluence 15 10 2009 11 10 z Confluence View Image Cell Number Loci Count Plate Thumbnails Growth Rate Summary Criteria Well A7 Data ini Area av T CUTE Ay 45 4 541 1 08 L Lud 1 100 10 000 1 06 1 08 Loci Area 2 actness Loci coun m EXPORT IMAGE SEQUENCE It is possible to export the sequence of images by clicking on the sequence with the right mouse button The sequence can be saved as a bmp jpg or png file The file will include the confluence percentage and time and day the image was acquired Molecular Devices 32 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL WELL DATA It is possible to click on a well in the list to go to its corresponding Well View and check if the colony is monoclonal There are three ways to move through the list and mark wells as monoclonal 1 Click the Yes button to mark a well as monoclonal and scroll to the next well image Click No to scroll to the next well without marking the well as monoclonal 2 Click on a well to view its image and click on the check box to mark it as monoclonal 3 Use the keyboard up down arrow keys to scroll through the wells and the spacebar to mark the wells The selected wells in the list can be saved by clicking on the Save Well List beneath the list This file can be saved as a csv file
52. llowing scenarios gt The selected results only have 1 time point Different Sets Of Wells Imaged The same set of wells was not imaged at each time point OK The Migration link is enabled in the following scenarios gt Fora time point series if different sets of wells have been imaged a message will appear informing that the migration application is unavailable and the Review Results screen will remain open to allow selection of other data gt Fora time point series if there is a mix of Full and Partial scans with the same plate barcode the following will happen If there is only one time point for each scan type the migration option will not be applicable and will be grayed out If there is only one Full scan data set and more than one Partial data set the migration will only be applicable to the Partial scan data and vice versa If there is more than one data set for both the Full and Results contain a mixture of full and partial scans Partial scan a message will appear allowing the selection of the Full or Partial scans Use Full Scans Yes Partial Scans Ma or Cancel For more information on the Migration application see pages 38 44 Ne Cancel Molecular Devices gt 24 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Analysing Results Once an imaging process has completed the results are displayed in the Results window which has several tabs Confluence View Image Cel
53. lls gt Open the Loci Count tab The well diameter can be adjusted if required gt Click Process to produce the loci counts for the selected wells The Loci Count tab screen will change to display an overview of all the selected wells and their corresponding loci count Confluence View Image Cell Number Loci Count Plate Thumbnails Growth Rate Summary gt As above in the monoclonality work flow click on a well to show the well image and gate out debris and misshapen colonies using the lower and upper sliders on the Minimum Area and Minimum Compactness histograms Confluence View Image Cell Number Loci Court Plate Thumbnails Growth Rate Summary EH LES te 6 days 17 15 hrs 9 days 17 12 hrs 4 days 18 33 hrs Criteria Well C1 Data Minimum Area 5 589 2 7 05 56 42 o2 1 1 100 10 000 1 06 1 08 Loci Area Minimum Compactness 4 33 83 5 96 872 G1wTl I 48 9 24 0 0 A 50 75 100 Loci Compactness Well Data Save Well List 14 Retum To Plate View Molecular Devices gt 52 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL gt Once satisfied with the gating of the data and the loci count subsequently produced the data can be exported The Well Data list is mainly used for accepting wells based on monoclonality so it is not necessary to check any of these well
54. lor and size of the fill area with a large red fill area representing a high cell number and a small blue fill area representing a low cell number A color scale is shown to the left of the graphic Hovering the mouse over a well displays a tool tip giving the well co ordinate and the estimated cell number for that well Formula Details Formula Name NS1 SELECT CELL NUMBER FORMULA This drop down menu will list all the formulas created for estimating the number of cells per well Remove Clicking this will remove the currently selected cell number formula from the drop down menu Edit Clicking this will allow editing to be carried out on To adjust the line click and drag the purple and orange squares To save the changes to the estimation formula click the Save button You can quit at any time by clicking the Discard button e 8 lici the currently selected cell number formula from the drop down menu A graph of cell number against confluence for the formula is displayed The handles at each end of the line can be dragged to edit the formula The formula is displayed at the top left and the edited version is displayed immediately below it Discard can be clicked to abandon the edits and return to the Cell Number tab or Save can be clicked to save the changes made to the cell number estimation formula The formula name can be changed in the top right hand box There is also the option to Regener
55. me Using the drop down menu or the arrows it is possible to toggle to the well of choice Well Confluence The well confluence percentage is displayed here for the selected well Focus Position The focus point of the image when captured is displayed here Brightness The brightness level used to capture the imaged is displayed as a percentage here EXPORT IMAGE It is possible to the export the currently displayed image in bmp jpg or png format If Show Confluence has been selected the confluence overlay is displayed with the exported image The zoomed position is saved within the image Molecular Devices 27 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Cell Number Tab This tab displays the estimated number of cells in each well both graphically and as a list The number of cells is estimated using a formula that can be created for each cell type from the confluence readings of a standard plate containing known numbers of cells See Appendix C for a detailed procedure Plate Type Greiner 96 well Barcode Ed CHO Cell Count Test Processing Type Cell Detection Method 1 14 06 2006 09 05 152 Confiuence View Image Cel Number Loci Count Piste Thumbnais Summary Select Cell Number Formula 200 480 NS1 z Remove F Edit Create New Well Cell Number Cell Number Each well contains a colored fill with the estimated cell number indicated by the co
56. must have read and write access to the c ProgramData Genetix Fusion CloneSelectImager config folder System Features Automated rapid confluence determination of cells growing in microplates Automatically plots time course of cell growth Cell number estimation Monoclonality indication Colony forming assay Fast scan and full scan modes Standard and high resolution imaging Exports data and images for further analysis Before Starting the safety instructions Then follow the procedures as set out in the Power Up section Before using the instrument is very important to read this manual and understand all Molecular Devices gt 5 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Hardware Guide Layout and Dimensions Indicator Lights The indicator lights show the status of the instrument Imaging Yacuum On Warning Plate Carrier The plate carrier consists of a glass plate surrounded by a vacuum bed seal The microplate is placed on the plate carrier so that the skirt is over the vacuum bed seal When the plate carrier retracts into the instrument for imaging two pushers gently push the microplate into the back right corner of the plate carrier so that the plate is always in the correct position for imaging Before imaging a vacuum is applied under the plate so that it is held down flat on the glass plate so that all the wells are in the same focal plane This obviates the n
57. ne of best fit To adjust the line click and drag the purple and orange squares iscar Cell Number Graphical Display window showing plotted data gt The line of best fit can be manually adjusted by dragging the handles at the end of the line The formula is displayed at the top left and the adjusted version is displayed immediately below it All cell estimate results are based on the adjusted version me or all of the cell Formula Details Please enter some numbers for the wells below 536 5234 5848 13 Formula Name Well Cell Number 52 100000 2 150000 2 25000 50000 D6 59 100000 150000 12500 2 25000 28 50000 100000 21 create save name for iscar Two lines visible showing the manually moved line in grey gt Assign a name to the data set in the Formula Name box gt Click Save to save the cell number estimation formula and return to the Cell Number tab Click Discard to abandon the changes Molecular Devices 62 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL gt The new formula can then be used to estimate cell numbers in plates containing the same cell type Appendix D Requesting a License If the following message is displayed after starting the CloneSelect Imager software a new license will need to be requested Create a license request and then e mail it to Customer Support License About To
58. ngs are changed Warning CloneSelect Imager is optimized for use with Microsoft Windows 7 and Connecting CloneSelect Imager The connections to CloneSelect Imager are on the connections panel on the left hand side of the instrument On off switch Ethernet connection Mains input Connect the mains cables to CloneSelect Imager the workstation and to the monitor before making the network connections The connection to CloneSelect Imager is a private Gigabit Ethernet link and the connection must be made to the workstation add on card Gigabit Ethernet port Molecular Devices gt 8 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Calibration and Alignment Calibration and alignment are performed by a Molecular Devices engineer before CloneSelect Imager is shipped If the instrument requires recalibration and alignment follow the procedure below Select the E Scope process on the Main Navigation screen Select the PetriWell W1500 plate as the plate to be imaged Start the run and insert the Fixed Cell plate shipped with instrument when prompted Align on to well Al of the Fixed Cell plate On the image selection screen select the lower left hand quadrant image of well D1 Adjust the focus until the cells on the Fixed Cell plate are in focus Image wells A12 and H12 and check that the focus is correct in each image focus should not be changed at this point just reviewed If the f
59. ocus is not correct contact Molecular Devices to arrange for the machine to be aligned Power Up Procedure The recommended power up procedure is Switch on CloneSelect Imager Wait for the Ready light to illuminate Leave CloneSelect Imager in the Ready state for more than 5 minutes prior to use in cases where the unit is cold to the touch wait for 30 minutes prior to use Switch on the workstation and start CloneSelect Imager software by clicking on the desktop shortcut The instrument is now ready for use yyy Rebooting CloneSelect Imager If the instrument has to be rebooted switch it off Wait for 30 seconds then switch on again Once the Ready light is illuminated the instrument is ready to run Molecular Devices gt 9 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Starting up CloneSelect Imager Before using CloneSelect Imager please refer to the relevant sections of this manual for important setup maintenance and safety information To start CloneSelect Imager software double click the icon on Windows desktop The software will connect to the instrument and display the Main Navigation Screen New Process Recent Processes CloneSelect Imager Processes Image Microplate Batch Microplate Imaging AS Image a microplate Image batches of plates with the same configuration a Review Results E Scope 2 Review the results of previous imaging runs Take single hi res im
60. option The current settings for the process are displayed grouped in categories Click on the category heading to call up a screen where the relevant settings can be altered via drop down lists Details The current process settings are displayed in drop down lists from which they can be edited directly Guide This option displays the process setup via a wizard style interface with Back and Next buttons to scroll through the settings If the options above are not used for editing the criteria the sections headers can be selected and drop down menus will be displayed for editing Molecular Devices 14 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Source Select the microplate to be imaged from the drop down list The list contains a number of compatible microplates from a variety of manufacturers If the mage Microplate desired plate does not appear in the drop down 7a ENS menu list contact Molecular Devices Summary Details Guide Image a microplate Well plates 96 well 1500 Barcodes Read barcode Enable or disable barcode reading by ticking the box If barcode reading is enabled and the instrument fails to read the barcode or barcode Review focus reading is not enabled a screen is displayed prompting for a barcode plate name to be entered manually The barcode name also be edited scar Tope Full Scan within Review Results at a later stage if required Enhance Images Auto
61. ording or otherwise without the prior written permission of Molecular Devices New Milton Ltd Information furnished by Molecular Devices New Milton Ltd is believed to be accurate and reliable however no responsibility is assumed by Molecular Devices New Milton Ltd for its use nor for any infringements of patents or other rights of third parties which may result from its use No license is granted by implication or otherwise under any patent rights of Molecular Devices New Milton Ltd Revised June 2011 Molecular Devices gt 69 of 69
62. perature 10 C to 40 C Humidity 20 to 80 non condensing Altitude Up to 2000M Mains supply 10 Rated Voltage Transient overvoltage Installation Category Overvoltage category II Rated pollution Pollution degree 2 Electrical Supply Voltage Power Connections Fuses 100 240V AC 50 60 Hz single phase 100VA IEC Input Fi Symbols on Equipment Symbol Meaning Beware moving parts Refer to user manual for operating instructions oor The year of manufacture is given the serial number label which is located on the rear of the unit European Economic Area EEA This mark on the product indicates compliance with the following EEC Directives 98 37 relating to The Supply of Machinery Safety Regulations 1992 89 336 EEC with amendments 92 31 EEC relating to Electromagnetic Compatibility 73 23 EEC the Low Voltage Directive Molecular Devices gt 57 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Appendix A Compatible Plate Types The standard CloneSelect Imager is configured to use the following plate types Manufacturer Catalogue number Well format Molecular Devices W1500 W1505 W1510 W1515 W1550 W1555 W1560 W1565 La WINS wi355 wi360 wi365 24 5 wise wssos WO wins waso wiss e woo Wis Win inso wios wios7 wose 1 11121022 mum Note manu
63. play Images Wells Selected Well gt Cc EGERIT Plotted Wells Migration Area mm e Time hr Select All Select 0 0000 mm 1 8110 mm Time Pnint 241hs B 24 1 hrs Note When changing the End Time Point only the selected time points will be displayed on the Thumbnails tab Data on the Overview tab is also recalculated using the selected time points Molecular Devices gt 44 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Molecular Devices gt 45 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Batch Microplate Imaging This process enables multiple plates to be imaged using the same configuration Summary Details Guide Batch Microplate Imaging Image batches of plates with the same configuration By clicking on the Setup header the appropriate plate type scan type and auto brightness option can be selected Auto brightness all plates option automatically selects Processing Type Call Detection the appropriate brightness for the image This can also be manually changed This process automatically looks for barcodes on plates but if these are not present a prompt will appear asking to manually insert a plate barcode name Once Start is clicked the process is the same as Image Microplate Summary Details Guide E Scope E Scope T
64. rch 71 C 87 Wy Organize m Views Ba Mew Folder tm Pade fac Mame Size Date modified Desktop k sS Recent Places Public Computer Documents Computer B ta Pictures Music A Network Recently Changed Searches Public SER SSRF EK Folders File name 8 4 1 81 19 2 Hide Folder The license request file was generated successfully The license request was saved to the file T XUsers andrea gough Desktop License Request req You must now send this file to your local Genetix support engineer They can then issue a new license file to you for you to install gt E mail this req file to a Molecular Devices representative gt Click Finish Molecular Devices gt 65 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Installing a License gt When a license file is received from a Customer Support representative save the file to a place accessible on the computer of your instrument gt Re open the CloneSelect Imager software gt Select Install a license file License will expire in 4 days This software requires a license to run You must first generate a license request file and send this to a support engineer who can then issue a new amp license to you jJ Request a new license Generate a license request file that a support enaineer can use to issue a new license Install a licens
65. rocess Button Opens the same Open Process dialogue box accessed by the File gt Open Process menu item Molecular Devices gt 13 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL CloneSelect Imager Processes This section explains in detail how to run processes on CloneSelect Imager Image Microplate This is the default process for imaging cells in microplates to determine confluence and carry out further analysis such as cell number estimation and monoclonality In the Main Navigation Screen clicking on Image Microplate or opening a previously saved Image Microplate based process will open the process Once opened a summary window will be displayed in order for the process criteria to be set up Imaging Criteria Setup Criteria for imaging a microplate are selected in this screen Summary Details Guide Image Microplate Current Process Ed Save process Image a microplate Save process as template o Close Process Create New Process Well plates 96 well W1500 Select from categories m4 From template From Read barcode Yes Review focus Yes Auto focus before run No Scan Type Full Scan Enhance Images Yes Processing Type Cell Detection Method 1 There are several options for selecting the way in which the process settings can be displayed for editing The following options can be selected for editing criteria Summary This is the default display
66. s Molecular Devices 36 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Summary Tab This tab displays a summary of the confluence data growth curve data and imaging credentials Plate Type Genetix 96 well Barcode 008638 Processing Type Cell Detection Method 1 13 09 2006 08 30 Confluence View Image Cell Number Loci Count Plate Thumbnails Growth Rate Summary 60 32 50 40 30 20 10 0 N of Wells 5 Confluence 44 25 75 Time Hours 50 Confluence Date Imaged Elapsed Time Operator i Mean Confluence 15 09 2006 08 36 4days 18 17 hrs nicola latchem 47 0 14 09 2006 08 17 3days 17 58 hrs nicola Jatchem 24 6 13 09 2006 08 30 2days 18 11 hrs nicola latchem 4 10 1 12 09 2006 08 48 18 29 hrs nicola Jatchem 53 11 09 2006 14 19 0 00hrs nicola Jatchem i 25 The table lists the Date Imaged Elapsed Time Operator Imaged on Min Confluence Mean Confluence and Max Confluence for each time the plate was imaged HTML REPORT This option enables a report to be as c generated containing the desired ao HTML Report Wizard information in HTML format ee d AN Various information such as Please select the sections that are ta be included in the report confluence growth rate cell number etc relating to the data can be selected to be included in the report 14 Confluence 14 Growth Rate Cell Number The loci data ar
67. s The data will be exported for all wells when exporting the data via the wizard Select the type of results that you want to include 1 Number Select Cell Number Formula 51 Loci Count May require time to generate data Loci Criteria Well Diameter 6 30 mm Minimum Area um Minimum Compactness Maximum Area 270134 24 um Maximum Compactness Histogram Bins p Colony area distribution Colony area and compactness for all colonies gt In the Data Export wizard the Loci Count option is selected and the criteria are automatically populated The default number of bins is 20 but in the example it has been changed to 5 bins The Colony area distribution and Colony area and compactness for all colonies are selected and Next is clicked to finish exporting the data 9 5 0 00 11 00 0 ii Barcode Exp 8 PlateType Greiner 96 Well WellRows 8 WellColumns 12 Operator Andrea Gough RunDate 29 10 2007 09 12 47 Annotation 96 wells have been imaged LociWellDiameter 6 30 LociMinimumArea 5589 LociMaximumArea 270134 LociMinimumCompactness 33 LociMaximumCompactness 88 Name Well Loci Count Mean Loci Area microns squared Count 5589 00 58498 00 Count 58498 00 111407 00 Count 111407 00 164316 00 Count 164316 00 217225 00 Count 217225 00 270134 00 A1 29 27178 85 41978 41712 34479 45914 38229 32922 49658 44808 39249 45797 45865 34832 50474 e Nea lt DNDN CO C5 CO sa
68. screen is displayed ready to continue Finish Clicking Finish will end the process The Image Microplate page will be displayed Once returned to this page there are several options available Save process will save the current process to the Recent Processes tab for future access Note A saved process can be changed Save process as template will save the current process to the Template tab for future access Current Process Note A saved template cannot be changed led Save process Save process as template e Close Process Close Process will close the process and return to the Create New Process Main Navigation Screen Results can be viewed via Review Results after closing From template the process see Review Results section From file There are also options to select and run a new process or a template from a saved location using the From template and From file locations Molecular Devices gt 20 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Review Results The Review Results process allows previous imaging runs to be reviewed and also to carry out further data processing such as confluence monitor cell growth cell number estimation monoclonality analysis and migration assay analysis When an Image Microplate process has completed the results are automatically displayed in a Review Results process Clic
69. uded or excluded from the growth rate output This is achieved by selecting the time point to include or exclude and clicking Apply The data will then either be included or excluded from the growth rate data All plate scans with the same barcode will be automatically included in the growth rate data unless excluded at this point Molecular Devices gt 35 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL GROWTH RATES 3 Print preview This list displays the Well Total Growth and close Mean Rate for each well the data set Genet Ss Well Brode 008538 PRINT This will print out a paper copy of the growth curves EXPORT This will enable the list of wells and the corresponding confluence for each time point in the growth curve to be exported as a csv or xml file The Data Export wizard will guide the process of exporting the confluence data The wizard provides the option to export the data for the following time points Select the type of results that you want to include Confluence 1 Cell Number Select Cell Number Formula NS Select which time points to export The curently selected time The most recent time for each well plate Loci Count May require time to generate data The complete time series 4 Criteria Cell Number and Loci Count data can also be exported at this point See the relevant sections for the description of exporting these data set
70. ular Devices gt 26 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL View Image Tab This tab displays the images for a Plate Type Gentix 96 well W1510 Barcode 005387 Processing Type Cell Detection Method 1 17 05 2010 08 39 selected well The whole well is Gnome ow os cat nur re estne ts men 1 1 so a 4 displayed 49 3 WELL SCHEMATIC By clicking on the image of the well currently being displayed it is possible to navigate to different areas of the well and this is reflected on the image schematic to the right The confluence levels of the currently 1 1 i Well Name selected whole well are displayed 27 D 9 e Focus Position 1 680 Brightness 497 below the schematic 5 ON Ra IMAGE TOOLS Zoom The slider can be moved either left or right to zoom out or in respectively The lowest magnification of the image is 18x and the highest is 144x When the figure turns red the system is zooming digitally and which may cause some pixilation of the image When zoomed into an image the zoomed area will be displayed on the image thumbnail to the right Contrast The contrast of the image can be improved by moving the slider to the left or right Show Confluence Checking this box will display the confluence detected within the well Detected objects are displayed in green WELL INFORMATION Well Na
71. ve folder once the arching has been performed Select this if the archiving is being carried out to free space on the C Drive Archive Molecular Devices 22 of 69 MOLECULAR DEVICES gt CLONESELECT IMAGER OPERATOR MANUAL Click Archive to start burning the results to CD DVD Archive to Network Disk Select Network Disk as the archive type Help Select an archive ype DVD Network Disk Archiving to Network Disk Select the location to which the data should Archive to Network or Disk be archived by clicking the Browse button To remove the data from the local archive after Archive Location it has been copied to the new location check the tick box Click the Archive button to begin archiving Remove local copy once move complete nha tn to CD DVD nter a name for the archive Select a media type CD A for a wiitable CD CD BWfor re witable CD DVDS for single layer writable DVD DVDS for a dual layer writable DVD To remove the stored image data from the computer when the disk has been written check the tick Click the Archive button to begin archiving Archive Location Either type in the location for the archived files or click Browse to display a Save As Dialogue to select the location Remove local copy once move complete If checked the results files are deleted from the C Image Archive folder once the archiving has been performed Select this if the arch
72. vement mm per hour between any two adjacent time points Plate Type Greiner 96 well 781098 Barcode 007055 Processing Type Cell Detection Method 1 Overview Thumbnails Well Details Migration Rate Total Migration Max Migration Rate Well wee c 5 Juniper mm mm mm h 0 1005 az A1 0 0004 0 0311 0 0012 A2 0 0013 0 0959 0 0024 0 0013 0 0919 0 0026 0 0014 0 1045 0 0019 0 0106 0 7684 0 0012 0 0013 0 0933 0 0024 0 0016 0 1189 0 0023 0 0016 0 1168 0 0025 OO0O00000000 Doos 00929 T 0 0018 0 1304 0 0033 00000 X X X Doos 05 0 0004 0 0313 0 0026 00000 7 5000 poos oom 0 0030 0 2132 0 0068 0 0037 0 2674 0 0085 0 0033 0 2384 0 0070 27 36 45 54 63 72 Time Hrs The table to the right of the heat map also displays these statistics for each well Click on any of the table headers to reorder the data It is possible to copy the heat map to the clipboard by right clicking anywhere on the map Click on any well of interest to highlight the well on the information table and on the Confluence graph Double click on any well of interest to hyperlink to the Well details tab Export The data for the well plate can be exported using this function A wizard will guide the Data Export process It is possible to export data for either Selected Time Points or for All Time points It is also possible to export the confluence data if required The data can be Molecular Devi

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