Covers preprocessing of calcium imaging videos, cell and activity trace extraction (supports the following methods: PCA-ICA, CELLMax, EXTRACT, CNMF, CNMF-E, and ROI), manual and automated sorting of cell extraction outputs, cross-session alignment of cells, and more.
Supports PCA-ICA, CNMF, CNMF-E, EXTRACT, and ROI cell extraction methods publicly along with CELLMax for Schnitzer Lab collaborators. Additional methods can be integrated upon request.
Most extensively tested on Windows MATLAB 2018b and 2019a. Moderate testing on Windows MATLAB 2015b, 2017a, 2017b, and 2018b along with OSX (10.10.5) 2017b and 2018b. Individual functions and CIAtah class should work on other MATLAB versions after 2015b, but submit an issue if errors occur. Newer MATLAB version preferred.
This repository consists of code used in and released with
G. Corder, __B. Ahanonu__, B. F. Grewe, D. Wang, M. J. Schnitzer, and G. Scherrer (2019). An amygdalar neural ensemble encoding the unpleasantness of painful experiences. Science, 363, 276-281. http://science.sciencemag.org/content/363/6424/276.
and similar code helped process imaging or behavioral data in:
J.G. Parker, J.D. Marshall, B. Ahanonu, Y.W. Wu, T.H. Kim, B.F. Grewe, Y. Zhang, J.Z. Li, J.B. Ding, M.D. Ehlers, and M.J. Schnitzer (2018). Diametric neural ensemble dynamics in parkinsonian and dyskinetic states. Nature, 557, 177–182. https://doi.org/10.1038/s41586-018-0090-6.
Y. Li, A. Mathis, B.F. Grewe, J.A. Osterhout, B. Ahanonu, M.J. Schnitzer, V.N. Murthy, and C. Dulac (2017). Neuronal representation of social information in the medial amygdala of awake behaving mice. Cell, 171(5), 1176-1190. https://doi.org/10.1016/j.cell.2017.10.015.
