Microscopy Image Browser Installation
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Contents
Run Microscopy Image Browser under Matlab environment
- Download Matlab distribution of the program (im_browser.zip)
- Unzip and copy im_browser files to im_browser directory in your Scripts folder. For example, c:\Matlab\Scripts\im_browser\
- Start Matlab
- Add im_browser starting directory (for example, c:\Matlab\Scripts\im_browser\) into Matlab path Matlab->Home tab->Set path...->Add folder...->Save, or alternatively use the pathtool function from Matlab command window
- Type im_browser in the matlab command window and hit the enter button to start the program
- Check System Requirements for further details about optional steps, such as use of Fiji, OMERO or use of DIPlib filters.
- Access help and tutorials from the menu of im_browser: im_browser->Menu->Help->Help
Run Microscopy Image Browser as standalone (Windows, x64 bit)
- Download standalone distribution of the program (im_browser_distrib.zip). Please note the version of Matlab (Matlab 8.4 (R2014b) for MIB version 0.998 and newer, or Matlab 8.1 (R2013a) for MIB version 0.997 and older) for which it was compiled
- Download and install MATLAB Compiler Runtime (MCR) that is compatible with the downloaded release of MIB
- Unzip im_browser_distrib.zip
- Start the file browser (Computer) and navigate to the directory where im_browser was unzipped (see image below). Type cmd.exe in the command line of the file browser to start the command prompt. Now the command prompt should start in the im_browser directory
- Start im_browser by typing MIB.exe
- It may take a while for program to start in this mode
- Access help and tutorials from the menu of MIB: im_browser->Menu->Help->Help
Note! If you want to use Fiji or Omero with the deployed version of im_browser you need to check java_path.txt file in the directory of im_browser.exe. Please modify this file and set correct path to your Fiji application and Omero Java libraries. See more about Fiji in the Fiji: Volume rendering and connection section
Run Microscopy Image Browser as standalone (MacOS, x64 bit)
Tested with Mac OS X (Yosemite), version 10.10.3 and Matlab version 8.4 (R2014b).
- Download standalone distribution of the program for Mac OS (im_browser_distrib_mac.zip). Please note the version of Matlab (Matlab 8.4 (R2014b) for MIB version 0.998 and newer) for which it was compiled
- Download and install MATLAB Compiler Runtime (MCR) that is compatible with the downloaded release of MIB
- Unzip im_browser_distrib_mac.zip to ./Users/[YourUserName]/Documents/MIB. Note! MIB will only work from this directory!
- Start im_browser by double click on ./Users/[YourUserName]/Documents/MIB/MIB_Mac.app using the Finder application
- It may take a while for program to start in this mode
- Access help and tutorials from the menu of MIB: im_browser->Menu->Help->Help
Note! If you want to use Fiji or Omero with the deployed version of im_browser you need to check java_path.txt file in the directory of im_browser.exe. Please modify this file and set correct path to your Fiji application and Omero Java libraries. See more about Fiji in the Fiji: Volume rendering and connection section
Additional info
im_browser stores its configuration parameters:
- Windows in c:\temp\im_browser.mat or when c:\temp is not available then the configuration parameters can be found in C:\Users\User-name\AppData\Local\Temp\im_browser.mat
- Linux in the script directory or in the local tmp directory (/tmp)
The configuration file is automatically created after closing of im_browser.
If im_browser does not start check Matlab path and/or delete c:\tmp\im_browser.mat file.
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