We strive to share our software with the scientific community. The most recent versions of our software are made available on this page.
SIMA (Documentation, Downloads, Example Dataset, GitHub)
The SIMA package is an open source Python package for analysis of fluorescence imaging data. We use this software for motion correction, segmentation, and extraction of fluorescence signals from 2-photon calcium imaging experiments.
ROI Buddy (Documentation, Downloads)
ROI Buddy is a graphical user interface for editing ROIs. It is designed to be used in conjunction with the SIMA package. See the documentation for installation details.
Kaifosh P, Zaremba J, Danielson N, and Losonczy A. SIMA: Python software for analysis of dynamic fluorescence imaging data. Frontiers in Neuroinformatics. 2014 Aug 27; 8:77. doi: 10.3389/fninf.2014.00077.
Kaifosh P, Lovett-Barron M, Turi GF, Reardon TR, Losonczy A. Septo-hippocampal GABAergic signaling across multiple modalities in awake mice. Nat Neurosci. 2013 Sep;16(9):1182-4. doi: 10.1038/nn.3482.