The set of ImageJ plug-ins included in this distribution form the mosaic processing software we use at NCMIR to process our large-scale brain maps and mosaics. The reason the software exists as ImageJ plug-ins is largely due to legacy and uses very little of the ImageJ functionality. Instead, the plug-ins makes substantial use of the Java Advanced Imaging and Image I/O libraries for most of the image processing and file I/O. Consequently, image files created with the mosaic processing pipeline generally are not fully compatible with the built-in functionality of ImageJ.

This distribution of ImageJ works only on Windows. Currently, we are not supporting other platforms.


Basic Requirements(All modules are included in download file)

Binary Download

Click here to download!

Install Instruction

Extract downloaded folder and execute “run.bat” inside extracted folder. You may need to adjust memory allocation for Java by editing “run.bat” file. In “run.bat”, you will see “--mx512m” option for 512MByte memory usage for Java. You can change this value for your environment.


Open "Index.html" file in "Documents" folder in extracted files or click here .

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