CALIMA: The semi-automated open-source calcium imaging analyzer

Highlights • Although calcium imaging is widely used in biological research, there are relatively few tools available for its analysis. These tools often enable only part of the analysis or require expensive software packages to run. Here we proposed the semi-automated standalone open-source software tool CALIMA, and we show that it is a valuable addition to the field of calcium imaging. As demonstrated with three highly different real-life datasets, CALIMA can detect cells and their activity with high sensitivity. CALIMA furthermore enables the user to reconstruct a network, and allows the user to limit the length of neuronal connections in said network. As some cell types grow neurites of limited length, the latter option can help to study the communication in groups of such cells.

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