Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Deep brain stimulation
BrainStimulator is a set of networks that are used in SCIRun to perform simulations of brain stimulation such as transcranial direct current stimulation (tDCS) and magnetic transcranial stimulation (TMS).
Developing software tools for science has always been a central vision of the SCI Institute.

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Most of our current software releases are now available through github. Our previous releases are archived here. Please follow the software links in the website menu to make certain you are getting the latest releases.

(Latest Version 2.1.367)

Released: August 15, 2014

File Product Version Size Distribution
chm-full-2.1.367.tar.gz CHM 2.1.367 27.1 MB Linux 64bit


  • chm-full is only for special situations and contains the entire source including image processing tools and panfish wrappers.

chm-source-2.1.367.tar.gz CHM 2.1.367 57.1 KB Linux 64bit


  • chm-source runs on any architecture (but easier on Linux64) with any MATLAB (at least R2011b) [requires a MATLAB license].

chm-compiled-r2013a-2.1.367.tar.gz CHM 2.1.367 12.3 MB Linux 64bit


  • chm-compiled runs on Linux64 only, without a MATLAB license (either with MATLAB R2013a or the free MCR R2013a). CHM Data 2.1.367 111 MB Linux 64bit


  • Training images and labels used in Perez, AJ., Seyedhosseini, M., Deerinck, T.J., Bushong, E.A., Panda, S., Tasdizen, T., Ellisman, M.H. (2014). A workflow for the automatic segmentation of organelles in electron microscopy image stacks. Frontiers in Neuroanatomy.

chm-example.tar.gz CHM Data 2.1.367 760.9 KB Linux 64bit


  • chm-example is an example of usage.