Microscopy Image Browser System Requirements

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Contents

Computer

Microscopy Image Browser is a program written under Matlab environment and it was tested to work under Windows/Linux/Mac installation of Matlab.

In addition compiled (standalone) versions of MIB are available for Windows and Mac 64-bit OS. The standalone versions of MIB may not have complete functionality of the original program but do not require to purchase Matlab license. The standalone MIB requires MATLAB Compiler Runtime (MCR) that will be 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 - R2020a.

Toolboxes

Bio-Formats

The Bio-Formats library brings support of multiple microscopy image formats. To use the library check the Bio checkbox in the Directory Contents panel of MIB.

Bio-formats java library (optional) is provided in the ImportExportTools/BioFormats folder.

BMxD Image Filters

When installed MIB can use BM3D and BM4D filters to filter datasets. The filters are not supplied with MIB due to license limitations and have to be installed separetly (only for Matlab version of MIB!).

Installation instructions:

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

Below are the datails of the installation process.

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.

Note 3, the Fiji 3D viewer may not work when started for the first time. In this case, Matlab should be restarted.

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:

Note! These files should be already pre-compiled for win32, win64 and mac64.

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:

  1. Installed Imaris and ImarisXT
  2. 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
  3. Restart Matlab

Note: it is recommended to put ImarisLib.jar to the static Java path of Matlab. To do that:

  1. Start Matlab and note the start-up (home) directory. For example: c:\Users\UserName\Documents\MATLAB
  2. Create javaclasspath.txt in this home directory and add path to ImarisLib.jar to 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
  3. 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:

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 im_browser\ImportExportTools\nrrd\compilethis.m.

OMERO: connection to OMERO server

Connection to OMERO server requires the download of OMERO API bindings for Matlab.

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.

For all other OS the files have to be compiled manually: Please refer to details in

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.

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:

Note! This file is already pre-compiled for win64.

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