GE Healthcare Life Sciencesincelldownload.gehealthcare.com/bin/download_data/... · GE Healthcare Life Sciences IN Cell Investigator Version 1.6.2 Release Notes June 28, 2013

GE Healthcare Life Sciences

IN Cell Investigator Version 1.6.2 Release Notes

June 28, 2013

IN Cell Investigator v1.6 rev02 Release Notes

1

Table of Contents

Product information 2

Operating systems supported 2

Installation requirements 2

Uninstalling Older Versions of IN Cell Investigator 5

Installing from CD-ROM 6

Installation 64-bit operating systems 6

Enhancements 11

Defects fixed 14

Known issues 15

Image Stitching Transformation: File Size Comparisons 18

Updates to IN Cell Developer Toolbox User Interface 19

Shading Removal QSM panel 19

New Protocol Wizard Data Management dialog 20

Enhanced control of memory allocation 21

IN Cell Investigator compatibility with IN Cell Compliance Manager 24

How to view macros in the Neurite Outgrowth context module 25

Accessing Workstation 3.7.2 Online Help 28

Upgrading to Info-ZIP 29

User Manuals 30


2

Product Information:

IN Cell Investigator v1.6.2 includes:

IN Cell Developer Toolbox v1.9.2

IN Cell Analyzer Workstation v3.7.2

Spotfire™ DecisionSite™ Client v9.1.1

IN Cell Translator v2.1

Operating Systems Supported

The latest version of the IN Cell Investigator is designed to support the following Microsoft Windows platform:

Windows XP Professional (Service Pack 2 or higher, 32-bit only)

Windows 7 (Professional, 32 and 64-bit)

Windows Server 2008 (Service Pack ;32 and 64-bit)

Windows Server 2008 (Release 2; 64-bit only)

Installation Requirements

Hardware

32-bit Windows XP Professional or Windows 7 (Professional

Windows XP Professional SP 2 or later or Windows 7 (Professional)

PC-compatible computer with a Pentium® 4(or later) microprocessor; Xeon® 51xx or later multi-core processor is recommended

High-resolution graphics display (at least 1024 x 768 x 24 bits); 2 monitors recommended

Minimum RAM size of 2 GB, 4 GB recommended

The paging file should match RAM size as indicated above

Minimum of 10 GB free disk space on the installation HD drive; 20 GB free space is recommended

Microsoft Internet Explorer 6.0 or higher with the following settings:

Security tab:

Internet zone - Security Level - "Medium" or lower

Trusted Sites zone - Security Level - "Medium" or lower

Privacy tab:

Settings - Medium level


3

64-bit Windows 7

Windows 7 (Professional)

PC-compatible computer with a 64-bit compatible dual-core microprocessor; Xeon 51xx or later multi-core processor is recommended

High-resolution graphics display (at least 1024 x 768 x 24 bits); 2 monitors recommended

Minimum RAM size of 4 GB for dual-core, extra 2GB per additional core recommended

The paging file should match RAM size as indicated above

Minimum of 10 GB free disk space on the installation HD drive; 20 GB free space is recommended

Microsoft Internet Explorer 6.0 or higher with the following settings:

Security tab:

Internet zone - Security Level - "Medium" or lower

Trusted Sites zone - Security Level - "Medium" or lower

Privacy tab:

Settings - Medium level

Software (Prerequisites applications will be installed, as necessary)

32-bit Windows XP

Microsoft Installer 4.5 At the Completing the Hotfix for Windows XP (KB942288-v3) Installation Wizard screen, check the “Do not restart now” checkbox and click Finish.

Microsoft .NET Framework 1.1


MSXML 4.0 SP2 Parser and SDK

Microsoft Visual C++ 2005 Redistributable Package

Microsoft .NET Framework 3.5 SP1

Microsoft .NET Framework 4

Microsoft SQL Server Express 2008 R2


4

32-bit/ 64-bit Windows 7






32-bit Windows Server 2008/64-bit Window s Server 2008 SP2







64-bit Windows Server 2008 R2








5

Uninstalling Older Versions of IN Cell Investigator

It is recommended that IN Cell Investigator v1.6.2 be installed prior to uninstalling earlier versions of the application.

During the installation process, a dialog will display indicating that Investigator has been detected on the computer. Click Yes in response to the question: Do you want to save your settings? This will be used to restore settings and data with the new installation.

Following the completion of the Investigator installation:

1. Navigate to the C:\Program Files\GE Healthcare\IN Cell Developer Toolbox 1.9.2 directory.

2. Locate and double click on the dtree_reg.bat file to register your flowchart.dll file to restore the saved settings in the current installation.

IN Cell Translator 2.1

The IN Cell Translator 2.1 application was updated with this release of IN Cell Investigator v1.6.2. You can choose to install or not install the update.

If you choose not to update to IN Cell Translator 2.1, confirm that the checkbox on the Select Features window of the installation wizard is unmarked.

If you choose to update to IN Cell Translator 2.1, with IN Cell Investigator v1.6.2, first uninstall IN Cell Translator 2.0 (if it was previously installed with IN Cell Investigator v1.6/v1.6.1). On the Select Features window of the installation wizard, mark the IN Cell Translator checkbox as shown above.

Note: If you attempt to update to IN Cell Translator 2.1 prior to uninstalling the application a warning message asking you to uninstall the older version. Clicking OK will allow the installer to complete without installing IN Cell Translator 2.1.


6

Installing from CD-ROM

3. Log on to Windows as an Administrator or as a User with Administrator privileges.

4. Insert the Investigator CD-ROM or double-click setup.exe.

5. If the ‘autorun’ feature is enabled in your computer, the InstallShield® Wizard will guide you through the installation process. Follow the instructions on the screen and enter or select the appropriate information when prompted. Alternatively, you can launch the InstallShield Wizard by double clicking the setup.exe file found in the directory of the CDROM.

6. When the Select Components dialog box appears, the following options display:

IN Cell Developer Toolbox

IN Cell Analyzer Workstation

Spotfire DecisionSite Client

GE Healthcare Software Licensing Server

IN Cell Translator

The checkbox is checked for each component that does not exist on your computer.

IMPORTANT: The Investigator installation process can be lengthy, and may take 15-20 minutes to complete – please be patient. Depending upon the speed of your system(s) this estimated time may be longer or shorter.

Installation on 64-bit operating systems

Windows 7 64-bit

When upgrading from IN Cell Investigator v1.6.1 to IN Cell Investigator v1.6.2, on a Windows 7 64-bit system:

1. Manually uninstall Microsoft SQL Server 2005 on the machine

2. Then reinstall Microsoft SQL Server 2005 with IN Cell Investigator v1.6.2


7

Windows Server 2008 64-bit R2

Important: The Windows Server 2008 R2 64-bit operating system is shipped with Microsoft .NET Framework 3.5.1. The warning message below displays when the installer tries to install .NET Framework 3.5.1. To bypass this warning, mark the .NET Framework 3.5.1 checkbox on the Server Manager screen, before installing IN Cell Investigator v1.6.2.

Procedure

If it is necessary to install Microsoft .NET Framework 3.5.1, follow the steps below:

1. Open the Server Manager.

2. Select the Feature option in the left panel, and click the Add Features option as shown below.


8

3. The Select Features window opens. Check the .NET Frame work 3.5.1 Features checkbox.

4. In the Add Features Wizard, click the Add Required Role Services button to add the role services.


9

5. The Web Server (IIS) window opens. Click the Next button.

6. On the Confirm Installation Selections window, click Install, to start the installation of .NET Framework 3.5.1.


10

7. The Installation Progress window displays.

8. The Results window displays on completion of the installation. Click the Close button the finish the install process.


11

Enhancements

Developer Toolbox v1.9.2

Set number of cores assigned to application for optimal performance

All processor cores are available for data analysis while allowing the user to set limits on the number of core used for analysis. The number of cores used for analysis may not exceed the user defined limit.

To set the limit on the number of core used during processing:

1. From the Settings menu, select More then select Multi-core processing.

2. On the Multi-core processing dialog, indicate the Number of cores assigned to application from the dropdown list.

3. Click OK.

4. Exit IN Cell Developer Toolbox 1.9.2 and then restart the application.

Note: Utilizing the highest number of cores available may not necessarily provide optimal performance. Theoretically, all applications are limited by the parallelized portion of the application. Therefore, you may achieve maximum reduction in computational time when assigning six to eight cores for the IN Cell Developer Toolbox application instead of 12 to 16 cores.

Translator v2.1

Time lapse feature has been added for multi-plate multi-well image stacks

The Time Lapse feature has been added allow images acquired from multiple plates with multiple wells over multiple times to be translated to time series image stack.

1. On the IN Cell Translator homepage, click the Time Lapse button.


12

2. The Time Lapse Stack Builder Wizard opens. Click Browse to navigate to the image stack folder. Click Next to continue.

3. All the images stacks found will be marked for inclusion in the time series conversion by default. Select the stacks for the time series conversion by unmarking the checkboxes as necessary.

4. To edit the Elapsed time between acquisitions, click in the Elapsed time field.


13

5. Click on the Plate Id field to open the Plate Split Options dialog. Select a range of

wells to create a sub-stack and click Add sub-stack to create the smaller image stack to convert.


14

Defects Fixed

Investigator v1.6.2

Defect Description/Fix

GE Healthcare License Server is not supported on Windows 64 bit operating systems

GE Healthcare License Server 64-bit version is available with IN Cell Investigator v1.6.2.



Group Summary fails to load large Analysis Data files. A message will display.

Workaround: If there is a memory shortage issue in the 32-bit application.

On a 64-bit OS computer, run the Group Summary64 from desktop icon.

OR

On a 64-bit OS computer, run SFConnect64 from the desktop icon to load XML files in Spotfire application and plat the data.

Run the Extended Focus transformation and attempt to run the Image Stitching transformation on the Extended Focus generated image stack fails.

Image Stitching can now be run on an Extended Focus generated image stack.

Unable to change colors for fused image when 3 wavelengths are used.

Application now allows you to switch colors when 3 wavelengths are used.

On the Define Fused Image dialog, the settings for each wavelength are lost when viewing/exporting overlay images from different wells

A Use channel settings option has been added. When checked, auto contrast will be done on channel contrast and not auto contrast adjusted images. These settings will be saved until manually changed by the user or a new stack is loaded.

Workstation v3.7.2


The Ex (Export to Excel) button on the Table toolbar is missing when IN Cell Workstation is run on the Windows 7 OS

The Ex button on the Table toolbar now displays as appropriate on Windows 7 computer.


15

Known Issues

Investigator 1.6.2

Known Description and/or Work-around When saving data onto external USB hard disks the error - insufficient disk space - error writing to a device" – appears in the log file. This is being noticed with large capacity disks (≥250 GB)

Problem is due to Microsoft's FAT32 specification that places a limit of 65K directory entries for the entire disk. Short file names (8 character length with a 3-character extension) use up a single entry, where long file names use more than one entry for each name which can drastically reduce the number of files that can be saved to the disk. Workaround: reformat the disk to use the NTFS file system (files limit = 4,000,000,000). Select the disk in Windows Explorer, and choose "Format" from the right click context menu NOTE: This is best done when the disk is new; otherwise data already stored on the disk will be lost.

When attempting to run Investigator 1.6.2 on a PC running Microsoft Windows 64 bit OS, a message displays from FLexLM stating that the HostID of the system does not match the HostID specified in the license file. The application does not start.

Workaround: After installing and licensing Investigator 1.6.2, perform the steps:

1. Open registry (Start->Run->Type Regedit->OK).

2. In Registry Editor navigate to: HKEY_LOCAL_MACHINE\System\CurrentControlSet\ Control\Session Manager\Memory Management

3. Rename AllocationPreference to AllocationPreference_Disabled.

4. Restart computer.

NOTE* This action should be completed also if any repair to installation is done.

When attempting to run Cell Tracking on a computer running the Windows 7operating system, the application fails if user is not included in the Administrator group

Workaround: To run Investigator as administrator, right click on the Investigator desktop icon, and select Run as administrator from the popup menu

If Microsoft SQL Server EXPRESS is already installed on the customer’s computer with an instance name other than SQLEXPRESS, Investigator 1.6 may fail to install SQL Server EXPRESS. The default instance name= SQLEXPRESS is used by the Investigator 1.6 application.

Workaround: Installation of Microsoft SQL Server EXPRESS will need to be done manually with default instance name= SQLEXPRESS.


16

IN Cell Translator will not launch when IN Cell Developer Toolbox is running with a network license.

Workaround: IN Cell Translator should be launched before IN Cell Developer Toolbox.

When attempting to create a summary using Group by a numeric value for large data sets, Group Summary presents the message Not Responding when processing for a long period.

Workaround: Do not exit the application. Group summary may take several minutes to several hours to process data depending on the number of data points in the data set. The user must wait for Group Summary application to respond with results or an error message before exiting.


Known Description and/or Work-around If the total size of the images used to perform Extended Focus transformation exceeds 60 GB, a memory shortage occurs

Workaround: If memory shortage occurs, it is recommended that you reduce the size of images used for the transformation

The Macros - Sieve operation and Post process - Sieve (binary) operation in User Defined Protocol are using different area object units. This unit should be the same.

In the current implementation, the Macros - Sieve operation is not dependent on calibration, and the object area is always defined in pixels. The Post process - Sieve (binary) operation in User Defined Protocol is dependent on calibration, and the object area is based on the calibration of the images.

The Cell Tracking - Particle Filter method generates an error if duplicate measures are found in the Protocol editor –Target set selected measures, and in the “Advanced Tracking Options” dialog

Workaround: Remove the duplicate measure from the target measure list, but keep the selection under the [Advanced tracking options] list.

If Linear Discriminant class definition is set to Four Area layout,

and the user rotates the threshold line past vertical position (90°) class positions will change. For example, if class "A" was at the left side of threshold line and class "B" was at right side, after threshold passes 90°, class "A" will be on right side of threshold line and class "B" at the left.

A warning message displays as soon as the threshold line passes the 90° position.


17

Developer crashes when an incorrectly translated stack (*.xgis) from IN Cell Translator is used. If the wavelengths are not

defined, , running a protocol with a Preprocess operation (Example: dilation) will crash the application.

Do not attempt to analyze incorrect translated stacks.

Enabling fusion for the third color, using an IN Cell 2000 image stack, with multiple wavelengths defined, triggers the message - “The filter names must be unique” - when OK or Apply are clicked on “Define Fused Image”, if the wavelengths are duplicated in the stack

Currently, fusion in Developer does not handle duplicate, identical wavelengths. Only different wavelength filters can be fused using the Define Fused Image dialog


18

Image Stitching Transformation: File Size Comparisons

Image stitching is the generation of a panoramic image from a set of overlapping images that capture different portions of the same scene.

The IN Cell Developer Toolbox has the ability to stitch overlapped images acquired from the IN Cell Analyzer 2000 large-chip camera, and analyze these stitched images.

The number of fields that can be stitched or analyzed is dependent on the virtual memory of the computer in use.

The table below summarizes the results of testing to determine the maximum numbers of fields that can be stitched for a 96 well plate, as well as the largest image file size that can be analyzed using different IN Cell Developer Toolbox protocols for a full 96 well plate. The highlighted rows indicate the optimal image file sizes for both 32-bit and 64-bit machines.

32-bit* - min RAM=2GB 64-bit** - min RAM = 4 GB

Assay/ Analysis Protocol type

% overlap # fields

acquired Image file

Size # fields

acquired Image file

Size

FYVE ; Granularity canned assay

10% 1 8.193 MB


10% 2 15 MB


10% 4 29 MB

FYVE; simple analysis; 1 row stitched

10% 6 43 MB

FYVE; simple analysis; 1 row stitched

10% 16 111 MB

Neurite CM 20% 4 29 MB



Neurite; Simple analysis; user defined

20% 16 102 MB

* Max output image size set as 60 MB Optimal image file size for 32-bit ** Max output image size set as 160 MB Optimal image file size for 64-bit

The above results are for 1x1 binned and normal 12-bit images. For 2x2 binned images, the above results hold for the same MB size of stitched images, and can be done with 4X as many of individual fields. Higher binning generates smaller file size (i.e., 2x2 binning allows 9 fields/well producing a 16 MB)

For deconvolved 16-bit images, the above results also hold if we deal with total MB of stitched image size


19

Updates to IN Cell Developer Toolbox User Interface

Shading Removal QSM panel

Three input fields were added:

Model – Select either the multiplicative or additive illumination model. The [multiplicative] option uses multiplicative model of signal distortions, whereas, the [additive] option uses additive model of signal distortions. The default is set to [Multiplicative]

Offset Value – Disabled when [Additive] illumination model is selected. For the [Multiplicative] model, specify the number of gray levels to be subtracted to correct the image (removes the effect of extra gray levels added during image acquisition). The default value is 100.

Differential Well Radius – Enabled when [Exclude Outer-Well Area] is selected. Sets the distance between the inner and outer well wall edges (in pixels). Positive values enlarge the difference, whereas negative values decrease the difference. The default value is 0.

One field was renamed:

The [Well Wall Removal] checkbox was renamed to [Exclude Outer-Well Area]


20

New Protocol Wizard Data Management dialog

One input field was added:

[Use stack name for data file] - saves the analysis data using the name of the image stack that was analyzed rather than the default filename.


21

Enhanced control of memory allocation

Analyses that generate a large number of targets may fail due to memory shortage. You, then, have the option stop analysis and save current result, or continue analysis risking the loss of data since Investigator accumulates analysis data in the memory.

The new memory allocation feature detects the condition when memory is almost full.

NOTE: Under the Windows 7-64 bit operating system, the IN Cell Investigator 1.6 application runs as 32 bit.

a. The 64-bit operating system provides more memory for application, such that many large image stacks that cannot be analyzed in one pass on Windows XP 32 can be on Windows 7-64 bit. b. Windows 7-64 bit is not without memory limitations, but it is several times larger than on 32 bit operating systems.

Memory storage is the fastest among storage devices. Drawback is that memory capacity is limited.

Developer Toolbox

1. If an analysis produces more targets than the user defined number, application warn a user that analysis continuation is dangerous. It may lead to memory shortage.

2. User has a choice: stop analysis and save current results or continue on user own risk. If user stopped analysis and saved partial results he may continue analysis from the well where analysis was interrupted.

NOTE: Critical number of targets varies from operating system to operating system and from protocol to protocol. Nevertheless it is possible to find number that works for multiple protocols on the same operating system.

3. To estimate critical number of targets following method can be applied. Run large stack till analysis crashes or produce message that memory shortage occurred. Multiply average number of targets in one filed by number of processed fields. Reduce resulting number by 15% - 20% and use as a critical target number.

4. To set the calculated average, click Settings|More|Set Critical Target Number from the Main menu


22

5. Enter the number of targets in the Critical Target Number field.

6. To turn off the feature, unmark the Use Critical Target Number checkbox.

7. To continue the analysis on a part of the stack, select a range of images to analyze from the list of images on the All Images tab. Highlight the start and end points of the range, and select Select Range (A) from the right-click pop-up menu. Then, open the right-click pop-up menu and select Create a New Subset (B).

8. Open the new tab containing the subset, and select Run analysis with current protocol from the Analyze dropdown list on the Component Overview panel.

B

A


23

9. Alternatively, select a well from the Plate View, select a well from where to restart, and select Analyze from current block from the Analyze dropdown list on the Component Overview panel.

Workstation

In Workstation, if the analysis produces more targets than the user defined number (memory limit is reached), follow these steps:

1. In the plate map, highlight the wells that were not analyzed by clicking on each well. Right-click on one of selected wells.

2. Select Run analysis on selected images (clear previous results) from the right-click pop-up menu on the Preview to continue the analysis from the point where it was halted.


24

IN Cell Investigator compatibility with IN Cell Compliance Manager

Lock/Unlock Protocols

IN Cell Investigator 1.6.1 applications, acquisition and analysis protocols can be locked, allowing users accessing these applications the ability to view and run the protocols. They may not be manipulated or edited.

The Lock/Unlock feature is enabled for the Administrator role ONLY.

IN Cell Developer Toolbox - click Lock icon on the Protocol Manager after selecting from Analysis|Protocol Manager menu. Conversely, clicking the icon a second time will toggle the feature to the Unlock status, allowing the analysis protocol to be manipulated.

IN Cell Analyzer Workstation - click the Lock icon on the Analysis Protocol Manager after selecting from Application|Analysis Protocol Manager menu. Conversely, clicking the icon a second time will toggle the feature to the Unlock status, allowing the analysis protocol to be manipulated.


25

How to view macros in the Neurite Outgrowth context module

The following example offers a procedure for viewing macros from the Neurite Outgrowth context module (CM):

1. Analyze using the context module, then close the window. Open Protocol Explorer and the underlying Developer Toolbox protocol displays.

2. In Cell Body and nuc target set there is a Postprocess macro attached. Click on Run Postprocess Macro and it shows this window. That’s the name of the macro applied to the target set.

3. Click on the Browse button and a new window appears which shows all the macros available.

4. A different macro can be substituted by selecting one of the options and clicking OK.


26

To edit or create a macro

1. From the Main menu select the Macro option:

NOTE: If the Macro option is not available, go to Settings|More|Macro Utilities to open the Macro menu bar option.

2. Select Edit to open the Macro Editor window.

3. Expand the Protocol Macros list. All the macros applied within the protocol are listed and will have a P. prefix.

NOTE: Other macros may be available, from other protocols, and will be displayed under Transform Point Operations (e.g., the HE, HE1 and HE2 macros are here).


27

4. To edit a macro, double click on the macro name. It will open in the Macro Editor window. In our example, this is the P.cell body and nuc macro. This is a complex 4-step macro, though some can be as simple as one step (e.g., Inversion function applied to transmitted light phase contrast images).

5. Double-click on one of the steps to open it and edit as necessary.

6. Click OK to save your changes and exit.

7. The macro will be automatically updated.


28

Accessing Workstation 3.7.2 Online Help

Microsoft Corporation no longer supports .hlp format help files under the Vista operating system. In order to access the existing IN Cell Analyzer Workstation 3.7.1 help text, the winhelp32.exe file must be downloaded from the Microsoft Download Center as noted below.

http://www.microsoft.com/downloads/details.aspx?familyid=6EBCFAD9-D3F5-

4365-8070-334CD175D4BB&displaylang=en

Copy and paste the winhelp32.exe file to:

Windows 32-bit C:\Program Files\GE Healthcare\IN Cell Analyzer Workstation 3.7.2

Windows 64-bit C:\Program Files (x86)\GE Healthcare\IN Cell Analyzer Workstation 3.7.2

Neurite analysis measurements available in Workstation 3.7.2

The following table should be used to supplement the information found in the Workstation 3.7.2 online help for the Neurite Analysis Measures.

Neurites (definition) - also known as debris; are sometimes found with no connection to any cell body and these are not counted The two types of measures correspond to the two types of connectivity – Type 1 = Neurites connected to only one cell body Type 2 = Neurites that connect to two or more cell bodies (one neurite that has connection to two or more cell bodies). Such neurites are divided by cell zone influence and parts are assigned to the closest cell.

Measure Definition

Neurite Count 1 number of neurites that connect to only one cell body

Neurite Count 2 number of neurites that connect to two or more cell bodies

Neurite Count Total Neurite Count 1 + Neurite Count 2

Area 1 total area of neurites that that connect to only one cell body

Area 2 total area of neurites that that connect to two or more cell bodies

Area Total total Area 1 + total Area 2

Skeleton length 1 skeleton length of neurites that connect to only one cell body

Skeleton Length 2 skeleton length of neurites that connect to two or more cell bodies

Skeleton Length Total Skeleton Length 1 + Skeleton Length 2

Branchpoints 1 number of branch points in neurites that connect to only one cell body

Branchpoints 2 number of branch points in neurites that connect to two or more cell bodies

Branchpoints Total Branchpoints 1 + Branch points 2

Width 1 average width of neurites that connect to only one cell body

Width 2 average width of neurites that connect to two or more cell bodies

Width Width 1 + Width 2

Branchpoint density 1 branch point density of neurites that connect to only one cell body

Branchpoint density 2 branch point density of neurites connected to two or more cell bodies

Branchpoint Density Branchpoint Density 1 + Branchpoint Density 2

Average area 1 average area of neurites that connect to only one cell body

http://www.microsoft.com/downloads/details.aspx?familyid=6EBCFAD9-D3F5-4365-8070-334CD175D4BB&displaylang=en

http://www.microsoft.com/downloads/details.aspx?familyid=6EBCFAD9-D3F5-4365-8070-334CD175D4BB&displaylang=en


29

Average Length 1 average length of neurites that connect to only one cell body

Average # of Branchpoints 1 Average number of branch points in neurites that connect to only one cell body

Form factor P2/4piS neurite form factor is a measure calculated by formula P2/4piS

Form factor P/Peff neurite form factor is a measure calculated by formula P/Peff (where Peff is effective perimeter)

Soma Area Ratio area of the soma (cell body) in relation to the entire area of the neurites 1 plus neurites 2

Soma Integrated intensity Ratio Intensity ratio of the soma structure = (neurite area 1 plus neurite area 2)/area of cell body (soma)

0B0BUpgrading to Info-ZIP

When analyzing large image stacks, the file compression at the end of the analysis can take a significant amount of time. To speed up this process, users may want to use Info-ZIP instead of 7-zip, the installed default compression tool.

Info-ZIP is about 4 times faster than 7-zip when compressing files. The trade-off is that the compression ratio is not as good as the one provided by 7-zip. Due to export regulations, it is not possible to include Info-ZIP as part of the default software installation. However, users can upgrade their system to use Info-ZIP:

To download Info-ZIP:

1. Open an Internet Explorer session.

From ftp://ftp.info-zip.org/pub/infozip/win32, download the files zip232xn.zip and unz552xn.exe.

2. Save the file, unz552xn.exe, to the Archiver subdirectory of the IN Cell Developer or IN Cell Workstation installation directory. Execute unz552xn.exe by double-clicking on it.

3. Extract the file, zip.exe, from zip232xn.zip and place it into the Archiver directory.

4. Open the Registry editor, and navigate to: HKEY_LOCAL_MACHINE\SOFTWARE\Imaging Research Inc.\Developer\1.9.1\Options

Change the [ArchiveType] entry from 'zip' to 'infozip'.

(In the case of IN Cell Analyzer, the Registry key is HKEY_LOCAL_MACHINE\SOFTWARE\Imaging Research Inc.\InCellAnalyzer1000 /

W\3.7\Options

The next time you start Developer or Workstation the Info-ZIP tools will be used.

LG3 files created with the ArchiveType 'zip' are completely interchangeable with LG3 files created with ArchiveType 'infozip'.


30

User Manuals

The user manuals for IN Cell Analyzer Workstation, IN Cell Developer Toolbox, and IN Cell Translator are included in the Manual folder of the CD-ROM. These are kept in separate PDF (Adobe® Acrobat format) files. These manuals are installed in the folder ‘…\Manual’ during setup. You will need Adobe Acrobat Reader v7.0 or higher installed on your computer to view or print the manuals. For your convenience, we have provided a copy of Adobe Acrobat Reader v7.0 on the CD-ROM. To install the reader, open the Acroread folder and run the AdbeRdr70_enu.exe program.


Customer/Technical Support

Asia Pacific Tel: +852 2811 8693 Fax: +852 2811 5251 Australasia Tel: + 61 2 9899 0999 Fax: +61 2 9899 7511 Austria Tel: 01/57606-1619 Fax: 01/57606-1627 Belgium Tel: 0800 73 888 Fax: 03 272 1637 Canada Tel: 1 800 463 5800 Fax: 1 800 567 1008 Central, East, & South East Europe Tel: +43 1 982 3826 Fax: +43 1 985 8327 Denmark Tel: 45 16 2400 Fax: 45 16 2424 Finland & Baltics Tel: +358-(0)9-512 39 40 Fax: +358 (0)9 512 39 439 France Tel: 01 6935 6700 Fax: 01 6941 9677 Germany Tel 089 / 96281 660 Fax 089 / 96281 620 Italy Tel: 02 27322 1 Fax: 02 27302 212 Japan Tel: +81 3 5331 9336 Fax: +81 3 5331 9370

Latin America Tel: +55 11 3933 7300 Fax: +55 11 3933 7306 Middle East & Africa Tel: +30 210 9600 687 Fax: +30 210 9600 693 Netherlands Tel: 0165 580 410 Fax: 0165 580 401 Norway Tel: 815 65 555 Fax: 815 65 666 Portugal Tel: 21 417 7035 Fax: 21 417 3184 Russia & other C.I.S. & N.I.S Tel: +7 (095) 232 0250 +7 (095) 956 1137 Fax: +7 (095) 230 6377 South East Asia Tel: 60 3 8024 2080 Fax: 60 3 8024 2090 Spain Tel: 93 594 49 50 Fax: 93 594 49 55 Sweden Tel: 018 612 1900 Fax: 018 612 1910 Switzerland Tel: 0848 8028 12 Fax: 0848 8028 13 UK Tel: 0800 616928 Fax: 0800 616927 USA Tel: +1 800 526 3593 Fax: +1 877 295 8102

Documents

GE Healthcare Life Sciencesincelldownload.gehealthcare.com/bin/download_data/... · GE Healthcare Life Sciences IN Cell Investigator Version 1.6.2 Release Notes June 28, 2013