An open source Java application for running and collecting real-time data from live animal experiments.

References:

Bowler J, Zakka G, Yong H, Li W, Rao B, Liao Z, Priestley J, and Losonczy A. behaviorMate: An Intranet of Things Approach for Adaptable Control of Behavioral and Navigation-Based Experiments. bioRxiv. doi: https://doi.org/10.1101/2023.12.04.569989

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.

(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.

References:

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.