ArcturusXT™ Microdissection Instrument Software Release Notes
Contents
1. gt applied biosystems ry l ke technologies Arcturus Laser Capture Microdissection System Arcturus Microdissection Instrument Software Release Notes For Research Use Only Not intended for any animal or human therapeutic or diagnostic use Information in this document is subject to change without notice APPLIED BIOSYSTEMS DISCLAIMS ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT EXPRESSED OR IMPLIED INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE TO THE FULLEST EXTENT ALLOWED BY LAW IN NO EVENT SHALL APPLIED BIOSYSTEMS BE LIABLE WHETHER IN CONTRACT TORT WARRANTY OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR SPECIAL INCIDENTAL INDIRECT PUNITIVE MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT INCLUDING BUT NOT LIMITED TO THE USE THEREOF WHETHER OR NOT FORESEEABLE AND WHETHER OR NOT APPLIED BIOSYSTEMS IS ADVISED OF THE POSSIBILITY OF SUCH DAMAGES TRADEMARKS The trademarks mentioned herein are the property of Life Technologies Corporation or their respective owners Nikon is a trademark of Nikon Corporation 2010 Life Technologies Corporation All rights reserved 4458771 Rev A 07 2010 Arcturus Laser Capture Microdissection Systems SOFTWARE RELEASE NOTES Arcturus 7M Microdissection Instrument Operating Software version 3 1 November 2008 Contents ASTM ATO MAST eio a RE TRE mm 1 New in Release v3 1 Nov2. Click Update Config Click Exit Install the fluorescence filter cube into the position defined in the HW Configurator 8 Log into the Arcturus operating software 9 The OPT Optional icon will be active in the Select pane When clicked the filter turret will move to the position assigned in the HW Configurator ers ga CT unies crt 2 Uncheck items that are not installed Turret positions for the items are fixed ow x I 1 Check the condensers that are installed Arcturus Laser Capture Microdissection LCM Systems 6 Arcturus V Microdissection Instrument Operating Software v3 1 Release Notes PN 4458771A 6 UV Laser Cutting Overlap Operating software v3 1 has added a small overlap of the UV cut line to ensure complete cutting during microdissection This overlap compensates for the rare event in which the UV laser initiation is delayed after a long period of system inactivation or following an illumination tower tilt This overlap of 10um applies to the first drawing item of any microdissection series only If there are several items to be cut within one action only the first will receive the small overlap Bug fixes in Release v3 1 1 The UV laser offset has been updated within the AutoScanXT software harvest function This will ensure that the UV is offset properly for the respective objective in use and ensuring that the UV cutting will occur efficiently 2 The Arcturus operating software
3. Ph icon again The diffuser will return to the position it was in prior to enabling Phase Contrast If it was In it will return to that position automatically If it was Out prior to using Phase Contrast it will remain in that position The condenser will also rotate back to the A position for brightfield illumination Note The motorized condenser option automates the movement of Phase Contrast components Remember to ensure that the Arcturus is properly set up for Phase Contrast illumination prior to use i Ensure both field and condenser apertures are fully open ll Rotate in the Bertrand Lens B located in the eyepiece turret of the binoculars ii View the phase plate black ring through the microscope oculars If needed focus the ring by rotating the screw located on the eyepiece turret to the right of the Bertrand lens selection See the Arcturus user manual for more detailed information on the user of Phase Contrast illumination Arcturus Laser Capture Microdissection LCM Systems 3 Arcturus M Microdissection Instrument Operating Software v3 1 Release Notes PN 4458771A 1 3 Motorized Differential Interference Contrast DIC DIC illumination requires that a number of items be put into place i Move the Polarizer into position ii Move the Analyzer into position ii Rotate the condenser to the DIC N1 position v Move the Diffuser to the Out position The motorized condenser option provide
4. the original instrument release version 1 1 0 0 Below is a list of new features and bug fixes included in the latest software release A ArcturusXT Zifaifxi File Edit View Image Microdissect Options Help Capture Drawing Items Groups A IR Spot Sizes Bl e Delete All o AutoScan Stored Positions Cap 4 Information ac Caps El Utm CapName Cap 4 G CapNotes Q O CapName D The name of this cap Arcturus Laser Capture Microdissection LCM Systems 15 Arcturus Microdissection Instrument Operating Software v3 1 Release Notes PN 4458771A New in Release v1 2 1 IR and UV Laser Location Indicators The IR and UV laser locations are now indicated by markers on the live video screen The green circle and blue cross mark the UV laser and IR laser locations respectively 2 Locate IR Laser from Top Level This feature allows the user to locate the IR laser from the top level without the need to enter the Microdissect Options Dialog box 2 1 Pulse the IR laser using the IR Capture Test Fire button in the Microdissect pane 2 2 Right click at the center of the IR LCM spot and select Located IR Spot The cross hair will appear to mark the updated location of the IR laser 3 More prominent drawing items UV Laser Location LE i IR Laser Location v Move stage Draw freehand Draw circle Draw line of IR Capture spots IR Capture Spot Select drawing item s Ruler
5. Capture Microdissection LCM Systems Click on Add New User A new line will appear in the main window showing the new user with generic information Enter the user ID that will be used when logging in Enter the user s full name and description if desired If this is not done the generic identifiers will remain Enter a temporary password for the new user If a password is not entered the generic password will remain Note It is recommended that the default password be changed after the initial login Enter the user category Administrator or Operator Administrator will have full administrative rights Operator will have access to all functions except User Maintenance and Calibrate Click Update to add the new user to the list This will update the user line in the main window with the new user information as entered Click Save Users to save all changes Repeat steps 1 6 for any additional new users When finished click the X in the upper right hand corner to close the window Arcturus M Microdissection Instrument Operating Software v3 1 Release Notes PN 4458771A User Maintenance Enable User Login feature Enable guest user login Login ID Category Name Description administrator Administrator administrator administrator steveb Operator Steve newuserl New User Setup 2 4 4 Calibrations E x nane Seve Remove use Password iewuserl Delete ALL aeo opea vi
6. Check the 1 5X box when the manual knob on the instrument has been rotated into place 2X Livelmage Mag 47 Arcturus Laser Capture Microdissection LCM Systems 13 Arcturus M Microdissection Instrument Operating Software v3 1 Release Notes PN 4458771A ensuring the two are properly synchronized Previous versions required the user to open the Inspect Options dialog to access the 1 5X selection This addition has simplified the process 3 Delete single spots in LCM Only object The user may now delete a single spot within an LCM only object Right click on the spot to be deleted and select Delete Spot Previous versions of software did not allow single spot deletions a within LCM only objects SPER Hove objects To Capture Group Located IR Spot 4 Move IR Spots to Different Capture Group The option to Move Objects to Capture Group has been added to the IR spot right click context menu The user may click on a single IR spot and choose to ME Se move it to another Capture Group Previous versions WY Delete spot of software did not allow this option for individual IR D E coe spots 5 Diffuser Position Saved The diffuser position is now saved upon exiting the Arcturus application Previous versions of software defaulted to the Diffuser In position when opening the software application With this release if the diffuser is Out it will remain out when the application is restarted Bug fixes i
7. Eraser Located IR Spot 3 1 UV Cut lines have been made thicker to be more noticeable upon the live image 3 2 Color filled IR laser spots The user may choose to Fill IR Spots This can serve to make IR spots more prominent on the live video screen and to differentiate the IR spots from a circle shaped UV cut object This selection can be made in the Capture Group Settings window accessible on the top level after clicking on a Capture Group letter or within the Select Options Dialog Box under the Capture Groups tab Capture Group Settings Mame Capture group A Annotation Default capture gro IH SpotColor BEES Blue UY CutColor EI Red Yes Fill lA Spot El Capture Cut Area FilllA Spot FI IPFI spots with color Arcturus Laser Capture Microdissection LCM Systems Arcturus Microdissection Instrument Operating Software v3 1 Release Notes PN 4458771A r f Fill IR Spot YES 16 4 LCM Only The user can select to designate an object as LCM Only such that will fill in the object with IR LCM spots independent of slide type being used The user may also choose to change Capture an object that has already been drawn from UV cut and IR At Groups capture LCM to LCM Only or from LCM Only to Cut and Capture 4 1 Select LCM Only on the Top Level If a membrane slide glass or frame is being used and indicated as such in the materials information
8. location on any slide Previous software versions allowed the Paste function only within the same field of view as the original object To paste an object 1 Click on the Select Object icon 2 Click on the object s of interest To select multiple objects hold down the lt Ctl gt key and click on each object Note Selecting an object automatically Copies that Delete Objects Delete Spots In Object object and makes it available for Paste There is not a LCM Only separate Copy function to select The selected item will Mowe Object s To Capture Group become bold IR Capture Objeck s i UV Cut Obj 3 Move to the area you desire to paste the object This apa can be anywhere on the current slide or anywhere Located IR Spot on the other two slides 4 Right click and select Paste Selected Object s 5 The object s will be pasted relative to the center of the live field of view where you selected Paste 6 lf you desired to adjust the position of the pasted object s select the object and drag to its desired location Note You may copy and paste objects in batches from a single live field of view so as to make it easier to paste and adjust the positions of those objects a Select Options x Tools Options IR Spot Sizes Capture Groups Drawing Items 11 Export Drawing Items information The user may export drawing item information from the Arcturus operating software into a
9. password protection so that users can save settings for future microdissection sessions Operating software version 3 1 now includes a User LogIn report The User Login report records the user the time of Login and Logoff as well as the total time spent while logged onto the system The report contains a running log of users and times of use The User Logln report is automatically saved at C data UserLogs folder Example User Logln Report 2008 10 16 16 11 52 Login schu 2008 10 16 16 18 56 Logoff schu time 00 07 03 Arcturus Laser Capture Microdissection LCM Systems 5 Arcturus M Microdissection Instrument Operating Software v3 1 Release Notes PN 4458771A 4 Tiled image and whole cap scan in AutoScanXT AutoScanXT is a purchasable option available only for the Arcturus instrument The AutoScanXT software module is an image analysis program that automatically identifies areas for microdissection based on user defined criteria AutoScanXT has been updated to allow image analysis of larger tiled images and the whole LCM Cap area The previous version allowed analysis of one field of view at a time This improved version allows for much faster processing of larger areas See the AutoScanXT User Manual for details on the software module and these above mentioned updates Hardware Configurator Updates A user login window has been added to the Hardware HW Configurator to prevent unauthorized access HW Configurator access is now l
10. text file To export the drawing item information open the Select Options dialog box and click on the Drawing Items tab Click the Save button r o Cut4rea Captured 540 986 799 382 746 164 0 Samannne wn 2 086 53 Ok cancel 12 Abort AutoScanXT Harvest function The user may quit the harvest function in the AutoScanXT software module by hitting the Escape lt Esc gt key When the harvest function is aborted the LCM and UV cutting actions will cease All objects will remain on the Regions list for subsequent harvest through the AutoScanXT module and also remain available for copy into the active Capture Group 13 Abort AutoFocus The user may use the Escape lt Esc gt key to abort the autofocus action Once the Escape key has been pressed the system will return to the original z position Arcturus Laser Capture Microdissection LCM Systems 11 Arcturus Microdissection Instrument Operating Software v3 1 Release Notes PN 4458771A 14 Power on or off the fluorescence illumination Source Sp inspec options xj at any time A nl wm Focus Magnification The user may now power on the fluorescence illumination source EXFO Microscope Lamp box at any time during the session Previous software versions required Intensity 38 tock the EXFO box to be turned on prior to initializing the Arcturus operating a o nlack software in order to control the functions throu
11. the software defaults to make any objects drawn as UV cut items with IR spots placed as tack points within The user may now designate objects to be captured using IR LCM spots only by checking the LCM Only box located in the Select Pane on the top level 4 2 Changing an Object from Cut and Capture to LCM Only Within an object drawn for cut and capture right click and select LCM Only The LCM Only line will be checked and the object will fill with LCM spots The Delete Object s Delete Spots In Object peripheral line will change to the color of the IR spot XS a P E x Move Object s To amp pture Group gt indicating the UV laser will no longer cut along this line A 4 3 Changing an Object from LCM Only to Cut and Capture If an object is already designated for LCM Only either by indication of a glass slide in use or by checking the LCM Only box in the Select pane see 4 1 above right click within the object and select LCM Only The LCM Only line will be UN checked The object will remain filled in with spots but the peripheral line will change color to the UV CutColor indicating the UV laser will now cut along this line If the user wishes to remove the spots they may right click Delete Spots in Object See 6 below and then place individual tack points as desired Arcturus Laser Capture Microdissection LCM Systems Arcturus Microdissection Instrument Op
12. Cnpbioarns Administrators have access to the Calibration window The Calibrations selection is available only when Load logged in as an Administrator Inspect Select Note It is recommended that any system calibrations Micradissect be conducted with the assistance of Life Technologies System 3 Trackball trained staff Please contact customer support before performing any calibration functions support moldev com 9 Double click to fire IR laser The user may now double click the mouse within the live image window to fire the IR laser This feature may be used to fire selectively over a single spot for capture or it may be used to locate the IR laser without the need to enter the Select or Microdissect options dialog windows To locate the IR laser double click within the live image window to fire the IR laser and then right click in the center of the IR LCM spot and select Located IR Spot The cross hair will appear to mark the updated location of the IR laser Arcturus Laser Capture Microdissection LCM Systems Arcturus Microdissection Instrument Operating Software v3 1 Release Notes PN 4458771A Calibrate User Maintenance Setup Stylus wo Move stage Draw Freehand Draw circle Draw line of IR Capture spots IR Capture Spat Select drawing item s Ruler Eraser Located T 10 10 Copying and pasting drawing items anywhere The user may copy and Paste any object s to any
13. Contrast Disabled x Please turn the appropriate condenser into position Please turn the condenser into position amp For brightfield m c 2 2 DIC When the DIC icon is clicked the diffuser moves to the Out position if required A pop up window will appear telling the user to remember to move the condenser to the required position DIC N1 and to move the Polarizer and Analyzer into position Differential Interference Contrast DIC Enabled x Reminder To visualize using DIC you must slide the Polarizer and Analyzer into the light path The Polarizer is located above Ehe condenser turret and the Analyzer is located beneath the Fluorescence Filter turret gr EE AN When the DIC icon is clicked again to disable DIC the diffuser moves back to the In position if required and another pop up window appears reminding the user to move the condenser back to the A position and to move the Polarizer and Analyzer out of the light path Differential Interference Contrast DIC Disabled x Remember to slide the Polarizer and Analyzer out of the light path when you are Finished with DIC visualization The Polarizer is located above the condenser turret and the Analyzer is located beneath the Fluorescence Filter turret pik f 3 User Login Report Released in operating software version 3 0 the User Login feature provides administrative privileges for the Arcturus and allows for the creation of user IDs with
14. aced if this value is zero 9 In previous versions the stage would move to a slide other than that in the live field of view after closing Load dialog This action has been updated so that when the Load options dialog box has been closed the live image will remain on the current slide position 10 Changes have been made in the calibration window to apply updated values for stage offsets and pixel micron immediately This eliminates the need to restart the software for the new values to apply 11 The Hardware configurator has been implemented so that users no longer need to manually edit XML files when changing objectives or making any modifications to the system configuration For details on the Hardware Configurator please contact Life Technologies technical support Release v2 0 November 2007 The primary goal for release version 2 0 is to release the AutoScanXT Image Analysis Software module This version also improves Arcturus usability and fixes bugs identified from the operating software release version 1 2 Below is a list of new features and bug fixes included in the latest software release New in Release v2 0 1 AutoScanXT AutoScanXT is a purchasable option available only for the Arcturus instrument and can only be activated with operating software version 2 0 The AutoScanXT software module is an image analysis program that automatically identifies areas for microdissection based on user defined criteria This program per
15. e Password to set a new password E ek O pU Change Password hew Password Fagge D Options Load Inspect Select Microdissect Calibrate User Maintenance Setup Stylus 2 i i _ Load e o Inspect Select Pa 7 Microdissect Logoff Calibrate 2 4 2 Enabling the User Login and Guest Login Features The user Login feature is disabled by default If you desire to utilize this feature you must first log in as the administrator and turn the feature on Once the feature is enabled the Login screen will appear each time you initialize the operating software The administrator may also choose to allow guest access to the system by enabling the guest access option When the Guest user login is enabled anyone can log in under the user ID Guest The Guest ID is general and uses a common user setting All users who use the Guest ID share the same user settings To enable the User Login and Guest User Login features the administrator must access the User Maintenance window and check the appropriate boxes To activate the Login feature once it is enabled the Arcturus operating software must be restarted User Maintenance El x User Login Enable User Login Feature Enable quest user login 2 4 3 Creating New Users To add users select the User Maintenance screen found in the options drop down menu 1 2 3 O Qo M Arcturus Laser
16. e next stored position appears in the active window To jump to that position click on the number or to move to other stored positions use the forward and reverse arrows per usual function 3 AutoScanXT training files are updated properly when a new one is created Version 2 0 did not properly refresh the training file list 4 In previous versions drawing items that had already been cut and captured and were then copied and pasted were cut and captured again Version 3 0 has corrected this behavior so the copied items remain in the complete status and not cut and captured again To reactivate those original objects follow the standard procedures outlined in the user manual 5 Software code has been updated to fix the handling of errors such as stage bump eliminating the potential for software crashes during this event 6 The calculation of captured areas has been updated to accurately perform the function after certain properties have been changed e g deleting IR spot change LCM Only property etc Arcturus Laser Capture Microdissection LCM Systems 12 Arcturus Microdissection Instrument Operating Software v3 1 Release Notes PN 4458771A 7 Software code has been updated to address errors that caused the appearance of a red X in the cap load and QC position 8 In previous versions LCM spots were still added inside drawing items even with SpotsPerCutLength 0 Version 3 0 has updated this so that no spots will be pl
17. ember 2008 cccc cece cece ee ence ee enna eee enaeeeeeaateesateeegaeeneaanens 2 Bug Fixes in Release V9sl usuras nando Rag quM Ad EIE KAREPUPAFEE MAPA RA ETUMAREEU NACE MAU CAE 7 Newin Release v3 O ApL2009 7 BUO FIXES iN Release Vg sie E EE ee 12 New in Release v2 0 November 2007 cccc cece cece eee eee e teen eee eee nene sese ese nnns 13 DUG FIXES Indieledse V2 E vase sacescseuxheebecatsecesessceossencienetensanuecnsseessmeueeean vente 14 New in Release v1 2 August 2007 cc ccc cece cece ence ee een e eee eee e eee teen essen nsns nans nnns 16 UG FIX SS IN in MARNE EE 22 Installation Instructions 1 Create a complete copy of the current Arcturus operating software folder C Program files Molecular Devices ArcturusXT 2 Rename the folder Copy of ArcturusXT X XXX This will allow you to revert back to the previous version in the event that there is an issue with the new version installation 3 Uninstall the current Arcturus software 4 Click on the link found on the Life Technologies website or run from the installation CD if provided 5 The Arcturus application and all files will be automatically saved and updated with settings saved from your previous version The current release version software can be found in the Software Updates section of the Arcturus Literature and Downloads page www appliedbiosystems com Arcturus Laser Capture Microdissection LCM Sys
18. erating Software v3 1 Release Notes PN 4458771A IR Capture Object s Paste Object s Located IR Spot Located UY Laser 17 5 Improved tiled image tool The user can now highlight the desired area for tiled images from any direction The previous release version allowed only top left to bottom right drawing The user may now highlight an area in any direction from the starting point TU m mE z i Take Tiled Image of Selected Area 6 Abort Quit if there is still a cap on the slide If the user tries to close the Arcturus application when an LCM cap is in place a pop up window will appear to provide the option to abort the application closure Cap Is Still On Slide lx Acap remains on a slide Do you still want to exit e IF you choose to exit the program will offload the cap First T Deleting spots from right click context menus The user can now select to delete a single LCM spot or all spots within an object by using the Right Click context menu Delete Objectis 7 1 When the user right clicks within an object but outside Delete Spots In Object an LCM spot there is the option to delete all spots LCM Only Delete Spots In Object or delete the entire object n Objeckis To Capt 5 Delete Object s ove Objeck s To Capture Group P IR Capture Objects LIV Cur Objeckrs Paste Objeckis Located IR Spot 7 2 When the user right clicks on a spot single spot or wit
19. f you want to end your session and keep the software application running or if you want to log off for another user to log in you must go to the Options menu in the task bar and select Logoff Once a user logs off all current settings are stored for that specific user When a new user successfully logs in the settings for the new user will be loaded including the following Capture group settings Cut and capture settings Visualization settings e Prior to logging off the user should remember to offload any cap remaining on the slide If a user logs off with a cap remaining it will be automatically offloaded to the QC position 2 4 Administrator Privileges 2 4 1 User Maintenance Window Administrators have access to the User Maintenance window in which new users may be created and existing users may be removed The User Maintenance screen can be accessed from the Options drop down menu The User Maintenance selection is only available when logged in as an Administrator When the menu item is selected a login screen will be presented again to prevent unauthorized use Arcturus Laser Capture Microdissection LCM Systems Arcturus 7M Microdissection Instrument Operating Software v3 1 Release Notes PN 4458771A User Log in ifi Please enter the UserID and Password Check Change Password to set a new password Change Password User Log in Ix Please enter the UserID and Password Check Chang
20. filter is selected the Arcturus fluorescence turret will move to the selected filter position as defined in the HW Configurator The selected filter cube icon will change color to indicate it is in position All available filter cube icons as designated in the HW Configurator will be bold Unavailable filter cubes will be grayed out and unavailable for selection in the operating software 1 2 Motorized Phase Contrast Phase contrast illumination requires that the proper phase annulus plate be in position in accordance with the objective in use Further for use on the Arcturus the diffuser must be in the Out position Without the motorized options in place the user must rotate the condenser manually to select the proper phase annulus plate and must go into the appropriate location within the operating software to change the diffuser position The motorized condenser option provides control of these functions through a single click of a button in the operating software Within the Inspect pane there is a Ph icon if the option is not active the icon is grayed out and unavailable When this icon is clicked the diffuser automatically moves to the Out position if required and the condenser rotates to the appropriate phase annulus plate according to which objective is in place Eos sd s ode n PhL 4x Ph1 10x 20x Ph2 40x 60x Liyehlmage Mag lt 7 To return to brightfield illumination click the
21. forms optimally with high contrast samples and is simple and straightforward to use With the software controls the user first selects typical regions of interest ROI s and background areas and then AutoScanXT employs these parameters to automatically identify areas in the sample for the microdissection process The information used to identify the areas for microdissection is stored in an AutoScanXT analysis file and can be used subsequently on other areas from the same sample or on other similarly stained tissue samples AutoScanXT also allows the combination of multiple analysis files enabling the complex analysis of samples with differences in staining intensities tissue thickness and variations in light intensities You may download Arcturus operating software version 2 0 on the Arcturus Literature and Downloads page of the website www appliedbiosystems com See the AutoScanXT User Manual for details on the software module 60x 2 1 5X magnifier The Arcturus microscope base has an option that allows you to increase the magnification of the current 1 0 objective to 1 5X The dial for this setting is located on the right side of the instrument above the manual focus knobs You must tell the Arcturus software you are using this feature on your microscope for the instrument to work correctly 40x 20x 10x To improve the feature usability a checkbox has been added to the top level of the GUI in the Inspect panel
22. gh the software If the EXFO box is not turned on prior to initializing the software and the user clicks on either the Fluorescence icon or opens the Fluorescence tab in the Inspect Options dialog Dox a pop up window will appear asking if the user would like the Arcturus software to take LU m UU control of the EXFO box The EXFO box can then be turned on and the D E m ul user can choose Yes take control through the Arcturus software or Exposure 300 No to maintain manual control of the EXFO box Fluorescence Device Not Found x The ArcEurusxXT software has nok detected the ExFO fluorescence device To connect the EXFO box Y you may perform one of the Following operations 1 To operate the EXFO box through the ArckurusxT software power on the EXFO box and click Yes Wait Far Ehe EXFO box ka warm up before use OR 2 To manually operate the EXF box power on Ehe EXFO box and click Mao Wait Far Ehe EXFO box bo warm up before use Bug fixes in Release v3 0 In previous versions the IR laser did not fire for copied and pasted items Version 3 0 corrects this so that the IR laser properly fires for all pasted objects 2 Stage moves are now suppressed when removing a stored position Previous versions would move the stage to the next stored position when one was removed causing confusion Upon deleting a stored position the stage remains in its current position while the number associated with th
23. gorized into two groups Operators and Administrators Administrators will have access to additional functions such as system calibration windows and user maintenance The user Log In feature is disabled by default If you desire to utilize this feature you must first log in as the administrator and activate the feature Once the feature is enabled the log in screen will appear each time you initialize the operating software See Section 2 4 2 Enabling the User Login and Guest Login Features for more details on feature activation Arcturus Laser Capture Microdissection LCM Systems 7 Arcturus M Microdissection Instrument Operating Software v3 1 Release Notes PN 4458771A 2 1 Logging in Once the Login feature has been enabled users and administrators are required to log in each time the software is opened Each user and administrator will have a unique User ID and Password Each time the Arcturus operating software is opened a login screen will appear Both the User ID and Password values are administrator for the default administrator account When the guest user login is enabled see below anyone may log in using the User ID Guest This User ID does not require a Password 2 2 Changing Passwords To change a Password enter the User ID and current Password and then check the Change Password box This will open the fields to enter the new Password Click OK to save the new Password 2 3 Logging Off I
24. has been updated to recognize when possible communication errors occurred This will prevent the operating software from freezing in such instances Release v3 0 April 2008 The primary goal for release version 3 0 is to include support of Arcturus instruments based on the Nikon Eclipse Ti microscope All versions from v3 0 on will support TE2000 and T based instruments This version also improves Arcturus usability and fixes bugs identified in operating software release version 2 0 Below is a list of new features and bug fixes included in the latest software release New in Release v3 0 7 Support for Nikon Eclipse Ti E microscope base The Arcturus microscope base has been updated to the Eclipse T E the latest offering from Nikon Version 3 0 of the Arcturus operating software and all versions going forward will Support both the Eclipse TE and the TE2000U platforms The software user interface remains constant between the two versions but there are various hardware interface changes Please refer to the Arcturus user manual for full details related the Arcturus Ti specific features and functions All items below pertain to the use of both the TE2000U and Eclipse T E systems 8 User Login feature The User Login feature has been created to provide administrative privileges for the Arcturus and to allow for the creation of user IDs with password so that each user can save settings for future sessions Users are cate
25. hin an LCM Only object there is the option to delete that single spot Delete Spot or the entire object Delete Object s Delete Spot Delete Spots In Object LEM Only Located IR Spat Delete Objects Arcturus Laser Capture Microdissection LCM Systems 18 Arcturus M Microdissection Instrument Operating Software v3 1 Release Notes PN 4458771A 8 Allow user to delete items with Delete key The user may use the Delete key on the keyboard in conjunction with the select tool icon to delete items on the live video image 9 Allow selection of multiple Drawing Items The user may select multiple objects within the Drawing Items list in the Select pane or on the live image in conjunction with the Select icon To select multiple items hold down the Ctrl key on the keyboard while using the mouse or interactive pen to click on multiple objects in the live image or multiple numbers in the Drawing ltems list Once selected the user may delete only those selected items in the Drawing Items list LEM Only Capture Drawing Items Groups E ul E ik H 5 Delete Object Delete Selected Objeck s IF Spot Sizes e Delete All a Auto cari 10 Pop up warning message if there is nothing to cut or capture A message will appear indicating that there are no objects to cut and or capture if that action is requested without any items drawn x There are no spots to cap
26. imited to administrator and service users The HW Configurator has also been updated to support the new motorization components The options will be configured upon installation by a trained engineer but the user may need to access this program if a custom filter cube is added to the Arcturus instrument The standard Red Green Blue and optional UV Triple Pass fluorescence filter cubes ArcturusxT will be in place and will have positions already assigned upon system installation if HW purchased with the original instrument anfigurator To add a User Defined fluorescence filter cube E ArcturusXT Hardware Configuration Ti base Peles Please close the ArcturusXT main application before using this hardware configurator 1 Click on the HW Configurator icon located on the Hardware Continue Nikon Motorization Arcturus operating system desktop gu re 2 Loginto the HW Configurator using the Position administrator or service information ia m prede a ae 3 Click on the Nikon Motorization Tab e T3 1 eck the intl furescenoe es 4 Check the box next to User Defined and enter the Uv a co HERR e position into which the cube will be placed c E Mese cc vit User Defined L cea Note One position must remain open in order to use brightfield illumination recommend position 6 Turret Ph DIC This section sets up the ae turret I installed on the instrument
27. inside the UV cut line is based on the diameter of the LCM spot Therefore ensure the accurate spot size is input within the Microdissect Options Dialog Box 14 Support dual operation of LC and LCM objects Objects tagged as LCM only will not be presented for cutting This feature gives the user the flexibility to set this tag On Off 15 UV Laser Bypass For safety reasons the UV laser is disabled when outside of the cap area However there may be applications for which the cap is not required or desired The previous release version did not allow Arcturus Laser Capture Microdissection LCM Systems 20 Arcturus Microdissection Instrument Operating Software v3 1 Release Notes PN 4458771A activation of the UV Laser Bypass The Laser Bypass function has now been enabled to allow UV cutting when a Cap is not on a slide To activate the UV Laser without a cap on a slide 15 1 Ensure the Bypass Key is in place in the back of the instrument The Laser Bypass will be orange indicating the bypass key is in place in the back of the instrument but the Laser Bypass icon has not been activated 15 2 Click on the Laser Bypass icon located in the Microdissect pane on the top level The icon will turn yellow indicating the UV laser is ready to fire Note For more information regarding the Laser Bypass feature and UV safety considerations refer to the Arcturus User Guide section 7 10 Microdissect Microdissect 16 Diffu
28. is In the example to the right selecting Delete Object will delete item PS BBL Sires Delete All 5 whereas selecting Delete Selected Object s will delete items 1 as e 3 and 4 4 The image brightness settings have been improved to ensure the settings remain when the user cancels out of the camera properties set up dialog window 5 The ruler position has been fixed to appear in the correct position when using digital zoom 6 The code handling the placement of LCM spots has been improved in several instances 6 1 The algorithm has been improved to ensure all LCM spots fall inside freehand and circle tool drawing objects 6 2 The edit function has been updated to ensure LCM spots fall inside object line after editing when using the circle drawing tool 6 3 The LCM Line tool has been improved to ensure the intervals between spots are consistent when drawing the line 7 The drawing tool now reverts to the grabby hand after completion of any operation within the Microdissect Tool pane i e cut capture etc 8 Improvements have been made to eliminate the potential loss of focus position when clicking around within the slide overview 9 The command to move to stored positions has been modified to check first if the current objective is allowed at the stored position and then to change to a lower objective if necessary This eliminates the potential for the objective to run into the underside of the stage when mo
29. n Release v2 0 1 Version 1 2 operating software moved the LCM Tack Points in from the UV cut line reducing the potential for collateral pick up It was noted in v1 2 that very small spot sizes were still being placed too close to the UV cut line and therefore improvements were made to move them further interior Note The distance the spot is placed inside the UV cut line is based on the diameter of the LCM spot Therefore ensure the accurate spot size is input within the Microdissect Options Dialog Box 2 he v1 2 Cut Capture function icon on top level in Microdissect panel was performing cut and capture on items that had been copied to other areas even when the original e object had already been cut and or captured The correct behavior is for only the new objects to be cut and captured This behavior has been corrected so that if an object that has already been cut and captured is copied and pasted to another area only that newly pasted object is available for cut and capture using the Cut Capture icon To cut and capture the old copied object the user must select the proper function from the drop down Microdissect menu bar at the top of the GUI screen 3 Abug was identified in v1 2 that prevented UV cutting when the user activated the Laser Bypass button with caps in load position This bug has been fixed and the laser bypass function works properly 4 Capture group changes in the Select Options box were not being updated in the InfoBox t
30. n activated and configured in the HW Configurator 1 1 Motorized Fluorescence The manual fluorescence filter turret is replaced by a mechanized turret which is controlled through the software Available filter cubes are represented by an icon within the Inspect pane of the operating software Filter cubes are selected by simply clicking on the desired icon Red Blue and Green filter cubes remain the standard inclusion with the purchase of the Fluroescence package Optional cubes including UV and Triple Dichroic may be defined within the HW Configurator as needed Users may introduce their own cubes see fluorescence cube specifications and are defined as OPT within the HW Configurator R Red Filter Cube G Green Filter Cube B Blue Filter Cube UV UV Filter Cube n a TP Triple Dichroic Filter Cube OPT Optional User Defined Cube R af efo e Fluorescence Filter Selection Arcturus Laser Capture Microdissection LCM Systems 2 Arcturus M Microdissection Instrument Operating Software v3 1 Release Notes PN 4458771A The standard fluorescence workflow still applies when using the motorized components except that the filter cube selection may now be done by the click of a software icon Please see the Arcturus user manual for complete fluorescence operational instructions Note Only five filter cubes should be allowed at any time since one blank position is needed for bright field imaging When a
31. op level GUI This has been updated so that any changes will be reflected in both areas 5 Spacing between IR spots was not correct when the spot radius was very small This has been updated to reflect correct spacing for all spot sizes Arcturus Laser Capture Microdissection LCM Systems 14 Arcturus 7M Microdissection Instrument Operating Software v3 1 Release Notes PN 4458771A 6 Certain commands require the objective to change to 2X so as to avoid collision with the stage Previous software versions did not restore the objective position after returning to the slide after these actions Changes were made to restore the current objective position after returning to the slide position 7 The commands to drive the cap move sequence have been updated so that the focus is properly lowered at all times that it should This change eliminates the potential for the objective to crash into the underside of the stage 8 There was an update to improve the action of moving to the center of a slide ensuring the proper location per the calibration settings 9 Afix was put in place to ensure the slide border on the slide overview is properly drawn at start of program 10 Updates were made to impose restrictions for the PresentStage command preventing the possibility of an objective crashing into the stage Release v1 2 August 2007 The primary goal for release version 1 2 is to improve Arcturus usability and address issues brought forth from
32. or to use i Ensure both field and condenser apertures are fully open ii Ensure the condenser is properly aligned extinction point achieved iii Ensure that the DIC sliders are installed beneath each objective to be used for DIC illumination See the Arcturus user manual for more detailed information on the user of Phase Contrast illumination 2 Manual Phase Contrast and DIC Updates The Ph and DIC icons may be used in the absence of the motorized components or when using the TE2000U based instruments When clicked the diffuser moves to the Out position as required for proper phase contrast and DIC visualization Alternately the user may still access the diffuser In Out button through the Inspect pane within the Illumination tab 2 1 Phase Contrast When the Ph icon is clicked the diffuser moves to the Out position if required A pop up window will appear telling the user to remember to move the condenser to the required position appropriate for the objective in place PhL 4x Ph1 10x 20x Ph2 40x 60x Arcturus Laser Capture Microdissection LCM Systems 4 Arcturus M Microdissection Instrument Operating Software v3 1 Release Notes PN 4458771A When the Ph icon is clicked again to disable Phase Contrast the diffuser moves back to the In position if required and another pop up window appears reminding the user to move the condenser back to the A position Phase Contrast Enabled x Phase
33. s control of some of these functions through a single click of a button in the operating software Within the Inspect pane there is a DIC icon if the option is not active the icon is grayed out and unavailable When this icon is clicked the diffuser automatically moves to the Out position if required and the condenser rotates to the DIC N1 position Live mage Mag 47 If the additionally optional DIC Analyzer Cube has been purchased and installed in the fluorescence filter turret when the DIC icon is a ef efo 7 OFT clicked the analyzer moves into position The user is required to move the Polarizer into position manually located above the condenser and if the DIC Analyzer Cube is not in use the Analyzer must also be pushed into position located below the objective nosepiece To return to brightfield illumination click the DIC icon again The diffuser will return to the position it was in prior to enabling DIC If it was In it will return to that position automatically If it was Out prior to using DIC it will remain in that position The condenser will also rotate back to the A position for brightfield illumination If the DIC analyzer cube is in use the fluorescence filter turret will also move back to an empty position Note The motorized condenser option automates the movement of DIC components during use Remember to ensure that the Arcturus is properly set up for DIC illumination pri
34. ser position saved The diffuser position is saved when using the Remember Settings and used when taking the overview image 17 Simplified software installation 17 1 Automatic XML update This utility will makes it unnecessary to manually backup and restore existing XML files to preserve instrument calibrations All files are updated automatically upon running the executable file 17 2 Hardware Configurator This utility eliminates the need to edit XML files during new software installation and makes easier the update of objective configurations once the software is already in place 18 Find UV focus tool This utility makes it easier to calibrate the UV focus during manufacturing and service Arcturus Laser Capture Microdissection LCM Systems 21 Arcturus V Microdissection Instrument Operating Software v3 1 Release Notes PN 4458771A Bug fixes in Release v1 2 1 General application performance and responsiveness has been improved 2 The IR and UV locate sequences have been improved to ensure cacti brightness settings remain constant during process LY Groups 3 Ambiguity has been eliminated in the process of deleting items from drawing items list There are now two selections in the right click context menu 1 Delete Object will delete the drawing item to which m the cursor points and 2 Delete Selected Object s will delete all bal highlighted object s within the list BOUE w Delete Selected Object
35. t technical resources and support information for all locations please refer to our Web site at www appliedbiosystems com
36. tems 1 Arcturus M Microdissection Instrument Operating Software v3 1 Release Notes PN 4458771A Release v3 1 November 2008 The primary goal of release version 3 1 is to include support for motorization on the Arcturus instrument and to provide improved utility for the AutoScanXT software module This version also improves Arcturus system usability and fixes bugs identified in operating software release version 3 0 Below is a list of new features and bug fixes included in the latest software release Note Arcturus operating software supports all Arcturus instruments based on the TE2000U and Eclipse T E microscopes New in Release v3 1 1 Support of Arcturus Motorization Arcturus instruments based on the Nikon Eclipse TE microscope released March 2008 may be configured with motorized system components These motorized options described below will be supported as part of operating software version 3 1 Note TE2000U based instruments are not compatible with motorization These motorized features will be available only on the Eclipse Ti E models of the Arcturus instrument There are three available motorized features 1 Motorized Fluorescence Filter Turret 2 Motorized Phase Contrast 3 Motorized Differential Interference Contrast DIC Motorized options are activated and configured in the Hardware HW Configurator see Section 5 Hardware Configurator Updates The instructions below assume the options have bee
37. ture make sure a cap is on the slide x There are no points to cut 11 Glass slide defaults to LCM Only If a glass slide is selected as the slide type the software will default the microdissection method to LCM Only Arcturus Laser Capture Microdissection LCM Systems 19 Arcturus 7M Microdissection Instrument Operating Software v3 1 Release Notes PN 4458771A 12 View total cut and capture areas in Drawing Items list Total cut and capture areas um have been added to the Drawing Items tab in the Select Options Dialog Box Individual items are listed along with the total areas for the cut and TR items a Select Options Tools Options f IR Spot Sizes Capture Groups Drawing Items Drawi ing Items Information A OB OC OD o Status Spots Cut4rea Captured New 43 64 060 30 395 New 4 385 1 414 New 0 9 309 New D 707 New 0 707 New D 707 New D 707 New n 707 68 945 44 651 ony one CO P2 9 13 LCM Tack Points moved in further from the UV cutting line The previous release version placed the IR Tack Points LCM Spot within a cutting object right next to the UV cut line This caused occasional pick up of unwanted material due to the actual LCM spot spilling outside the UV cut line The algorithm has been updated to place the tack points more interior further away from the UV cut line eliminating the potential for collateral pick up of material Note The distance the spot is placed
38. ving to the stored position 10 The bug has been fixed that prevented the selection of an object or drawing item in specific conditions 11 The software step to check if the video driver is OK has been moved to precede the hardware initialization steps home stage focus etc 12 The bug has been fixed which caused the UV laser to not power on in some situations i e after tower tilt condition 13 A fix has been implemented to eliminate cap handling errors when a cap is placed too close to the left edge of a slide 14 The eraser tool has been corrected to properly handle erasing of parts of a LCM Lines 15 The calibration window has been updated to correct the position of the crosshairs in related windows in which they were slightly off center 16 The function of the microdissect button has been updated so that the cap will not be picked up and moved if all drawing items are within the cap area 17 Clicking on an item in the item list should always move that item to the center of the screen regardless of the number of objects in the list Arcturus Laser Capture Microdissection LCM Systems 22 Arcturus M Microdissection Instrument Operating Software v3 1 Release Notes PN 4458771A Part Number 4458771 Rev A 07 2010 gt applied w biosystems by Life technologies Headquarters 5791 Van Allen Way Carlsbad CA 92008 USA Phone 760 603 7200 www lifetechnologies com Technical Resources and Support For the lates
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