Microscopy Image Browser System Requirements
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Contents
- Computer
- MATLAB
- Toolboxes
- Bio-Formats Library for Microscopy Image Formats
- BMxD Image Filters
- FIJI: volume rendering and connection
- FRANGI: compiled Frangi mask filter
- IMARIS: connection to Imaris
- Membrane Click Tracker
- NRRD: read NRRD format
- OMERO: connection to OMERO server
- Random Forest Classifier
- SLIC superpixels, supervoxels and maxflow the Brush tool with supervoxels and for Graph-cut and Classifier
- Software Volume Rendering in MIB
Computer
Microscopy Image Browser is a program written in the MATLAB environment and has been tested to work on Windows, Linux, and Mac installations of MATLAB
In addition to the MATLAB version , there are also compiled (standalone) versions of Microscopy Image Browser available for Windows, Mac and Linux 64-bit operating systems. These standalone versions may not have the complete functionality of the full MATLAB version but can be used for academic research without requiring the purchase of a MATLAB license.
The standalone MIB requires MATLAB Compiler Runtime (MCR) that is automatically installed during installation.
It is highly recommended to use 64-bit operating system with sufficient amount of memory.
MATLAB
MATLAB, Release 2014b, (original MIB version 2.00; the newer versions of MIB may require R2017a or newer).
MIB was tested with MATLAB R2014b - R2022a.
DeepMIB is available for R2019b but the newer releases are recommended
Toolboxes
- Image Processing Toolbox, V7.0 (R2010a) or newer is REQUIRED
- Parallel Computing Toolbox, R2019b or newer is recommended
- Computer Vision Toolbox, (required for DeepMIB, MATLAB R2019b and newer) for training of 2D, 3D CNNs and segmentation of datasets
- Deep Learning Toolbox, (required for DeepMIB, MATLAB R2019b and newer) for training of 2D, 3D CNNs and segmentation of datasets
- Statistics and Machine Learning Toolbox (optional) for alternative to the Random Forest classifiers
- Statistics Toolbox (optional) for alternative to the Random Forest classifiers
- Optimization Toolbox (optional) for alternative to the Random Forest classifiers
- Computer Vision System Toolbox for automatic alignement using detected image features and for Deep MIB (MATLAB R2019b or newer, MIB version 2.70)
Bio-Formats Library for Microscopy Image Formats
The Bio-Formats library is a software tool developed by the Open Microscopy Environment (OME) that provides support for reading and writing multiple microscopy image formats.
In the context of MIB, you can enable the Bio-Formats library by checking the [✓] Bio checkbox in the Directory Contents panel. This allows MIB to utilize the Bio-Formats library to read and import microscopy image data in various formats.
Bio-formats java library is provided in the ImportExportTools/BioFormats folder.
BMxD Image Filters
MIB has the capability to use BM3D and BM4D filters for filtering and enhancing your microscopy image datasets filter datasets. However, it's important to note that these filters are not supplied with MIB due to license limitations. Therefore, if you want to use BM3D and BM4D filters with MIB, you will need to install them separately.
Installation instructions
- Download BM3D MATLAB software and BM4D MATLAB software from Image and video denoising by sparse 3D transform-domain collaborative filtering webpage.
- Unzip the files to directory with MATLAB scripts. For example, c:\MATLAB\Scripts\BMxD\BM3D and c:\MATLAB\Scripts\BMxD\BM4D
- Start MIB and specify these folders in MIB preferences: MIB->Menu->File->Preferences->External dirs
- Restart MIB
FIJI: volume rendering and connection
Microscopy Image Browser can use Fiji 3D Viewer plugin for visualization of volumes and models. In addition, there is a Fiji Connect panel that allows interaction between MIB and Fiji.
!!! Warning !!!
It seems that Fiji 3D viewer is not compatible with MATLAB on MacOS, please do not change write permission for the sys\java\jre\win64\jre\lib\ext on the MacOS
Installation process
- Download Fiji [link] (for MIB older than 2.60 use the Fiji Life-Line version, 2015 December 22)
- Unzip and start Fiji (fiji-win32.exe or fiji-win64.exe)
- Update Fiji: Fiji->Menu->Help->Update Fiji (it may be required to repeat this step one more time after restart of Fiji)
- In the Fiji folder should appear a folder scripts with the Miji.m file
- The scripts sub-folder containing Miji.m should appear within the Fiji folder
- Start MATLAB
- Start MIB and open the Preferences Window: MIB->Menu->Preferences->External dir. Add path to the Fiji installation folder there, for example as C:\Tools\Fiji.app for Windows or /Applications/Fiji.app/ for Mac OS
Important notes
Note 1, the following MATLAB path should be open for writing:
...\MATLAB\sys\java\jre\win64\jre\lib\ext and ...\MATLAB\sys\java\jre\win64\jre\bin
Note 2, 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.
FRANGI: compiled Frangi mask filter
Compiled Frangi Mask filter is recommended for faster run. Please compile it for your OS. Most of C-functions can be compiled using a single script:
Compilation details
- In MATLAB command window change directory to mib\Tools\, where mib is the path where MIB was installed, for example c:\MATLAB\Scripts\mib
- To compile, type in MATLAB command window mib_compile_c_files
IMARIS: connection to Imaris
Microscopy Image Browser can be used together with Imaris. This functionality is achieved with IceImarisConnector written by Aaron C. Ponti, ETH Zurich.
Requirements:
- Installed Imaris and ImarisXT
- Add path of Imaris installation to a system environment variable IMARISPATH. Start->Computer->right mouse click->Properties->Advanced system settings->Environment Variables...->New.... For example, IMARISPATH = c:\Tools\Science\Imaris\. Also path to Imaris can be specified from the MIB preferences: Menu->File->Preferences->External dirs
- Restart MATLAB
Additional notes
Note: it is recommended to put ImarisLib.jar to the static Java path of MATLAB. To do that:
- Start MATLAB and note the start-up (home) directory. For example: c:\Users\UserName\Documents\MATLAB
- Create javaclasspath.txt in this home directory and add path to
ImarisLib.jarto this file (for example, c:\Program Files\Bitplane\Imaris x64 8.0.2\XT\matlab\ImarisLib.jar). One way to do that (Windows) is to type in the MATLAB command prompt: system('notepad javaclasspath.txt'); add the path; and save the file - Restart MATLAB
Membrane Click Tracker
Compiled files are required to use Membrane Click Tracker tool. Please compile them for your OS. Most of C-functions can be compiled using a single script
Compilation details
- In MATLAB command window change directory to mib\Tools\, where mib is the path where MIB was installed, for example c:\MATLAB\Scripts\mib
- To compile, type in MATLAB command window mib_compile_c_files
Note! These files should be already pre-compiled for win32, win64 and mac64.
NRRD: read NRRD format
Microscopy Image Browser uses an own function for saving data in the NRRD format, but relies on Projects:MATLABSlicerExampleModule by John Melonakos for reading it. On Windows OS the files should be already pre-compiled, but for Linux it may be needed to compile them.
Please refer to details in mib\ImportExportTools\nrrd\compilethis.m.
OMERO: connection to OMERO server
Connection to OMERO server requires the download of OMERO API bindings for MATLAB.
Installation details
- Download MATLAB plugin for OMERO from here. It should be listed in the OMERO->OMERO Downloads, Plugins/MATLAB section. (Note! Make sure that the version of MATLAB plugin corresponds to the version of OMERO server you are going to login. Old OMERO downloads are listed in the Previous versions section at the bottom of the page.
- Unzip the file to your scripts directory, for example C:\MATLAB\Scripts\OMERO_5
- FOR MATLAB VERSION Add this directory (C:\MATLAB\Scripts\OMERO_5) with subfolders to MATLAB path (MATLAB->Home tab->Set Path...->Add with Subfolders...) or run pathtool in MATLAB command window
- FOR DEPLOYED VERSION Add path to the OMERO installation using the MIB Preferences dialog: MIB->Menu->Preferences->External dirs. For example, C:\MATLAB\Scripts\OMERO_5\libs\ for Omero version 5, or C:\MATLAB\Scripts\OMERO_4\libs\ for Omero verison 4
When using Omero, MIB stores servers and ports in mib_omero.mat file located in c:\temp\mib_omero.mat or in the system temp folder.
Random Forest Classifier
Compiled files are required to use Random Forest Classifier. Microscopy Image Browser uses randomforest-matlab by Abhishek Jaiantilal which is already compiled for win32, win64.
Compilation details
For all other OS the files have to be compiled manually: Please refer to details in
- mib\Tools\RandomForest\RF_Class_C\README.txt
- mib\Tools\RandomForest\RF_Reg_C\README.txt
SLIC superpixels, supervoxels and maxflow the Brush tool with supervoxels and for Graph-cut and Classifier
The brush tool can be used to select not individual pixels but rather groups of pixels (superpixels). This functionality is implemented using the SLIC (Simple Linear Iterative Clustering) algorithm written by Radhakrishna Achanta et al., 2015. In addition the SLIC superpixels and supervoxels are used for the Graph-cut segmentation and Classifier.
For the Graph-cut segmentation MIB is utilizing maxflow 2.22 written by Yuri Boykov and Vladimir Kolmogorov.
Compilation details
- In MATLAB command window change directory to mib\Tools\, where mib is the path where MIB was installed, for example c:\MATLAB\Scripts\mib
- To compile, type in MATLAB command window mib_compile_c_files
Note! These files should be already pre-compiled for win32, win64 and mac64.
Software Volume Rendering in MIB
Compiled affine_transform_2d_double.c function is required for volume rendering. Please compile it for your OS. Most of C-functions can be compiled using a single script. This file is already pre-compiled for win64.
Compilation details
- In MATLAB command window change directory to mib\Tools\, where mib is the path where MIB was installed, for example c:\MATLAB\Scripts\mib
- To compile, type in MATLAB command window mib_compile_c_files
Note! This file is already pre-compiled for win64.
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