Microscopy Image Browser Troubleshooting
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MIBdoes not start -
Out of memory -
Fiji: reports Java3D is not installed. -
Fiji: Failed to retrieve Exception Message -
Hotline
MIB does not start
- Check that
MIBdirectory is in MATLAB path:File->Set path.... If it is missing, add it with->Add with Subfolders-> Save. - Delete old configuration file:
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for Windows - C:\Users\Username\MATLAB\mib.mat or in the Windows TEMP directory (C:\Users\User-name\AppData\Local\Temp\). The TEMP directory can be found and accessed with
Windows->Start button->%TEMP%command - for Linux - /home/username/Matlab or local TEMP directory
- for MacOS - /Users/username/Matlab or local TEMP directory
Out of memory
When working with large datasets it is normal to experience shortage of available memory. The following recommendations could be considered:
- Use 64-bit operating system. The 32-bit operating system can use only up to 3.25 Gb.
- Use 8-bit datasets. Convert from 16-bit to 8-bit via
Menu->Image->Mode->8 bit. - Use Models with 63 maximal materials,
Menu->File->Preferences->Models-> Number of materials in a model->63. - Lower number of 3D Undo steps in the Menu-File->Preference dialog>.
- Lower number of maximal steps to keep in the Undo history Menu-File->Preference dialog>.
- Completely disable Undo history in the Menu-File->Preference dialog>.
- Turn off
Selectionlayer from theDisable selectionoption of the Menu-File->Preference dialog>. Note! when theSelectionlayer is switched off it is not possible to do the segmentation.
Fiji: reports Java3D is not installed.
Most likely there are no write permissions to some folders required for automatic installation of Fiji 3D viewer. Please check carefully the MATLAB command window, where Fiji reports required directories.
For example in standard case the following directories should have write permissions:
- C:\Program Files\MATLAB\MATLAB Compiler Runtime\v81\sys\java\jre\win64\jre\lib\ext
- C:\Program Files\MATLAB\MATLAB Compiler Runtime\v81\sys\java\jre\win64\jre\bin
Fiji: Failed to retrieve Exception Message
If the Failed to retrieve Exception Message error appears, please increase the heap space for the Java VM in MATLAB, see details here.
For example, rendering of 1818x1022x717 volume requires 4Gb heap size.
Hotline
For bug reports please use the im-browser issues system: <https://sourceforge.net/p/im-browser/tickets/ https://sourceforge.net/p/im-browser/tickets/>.
For additional support please use the mailing list: <https://lists.sourceforge.net/lists/listinfo/im-browser-support https://lists.sourceforge.net/lists/listinfo/im-browser-support>
Ilya Belevich (ilya.belevich @ helsinki.fi)
web site
Institute of Biotechnology
University of Helsinki
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