Imaging analysis tools A table containing imaging analysis tools for biology and neuroscience, with a focus on calcium imaging. Up-to-date table at https://github.com/bahanonu/imaging_tools. Created by Biafra Ahanonu, PhD (HHMI Hanna Gray Fellow, Basbaum Lab, UCSF). The table can also be found at: https://bahanonu.com/brain/imaging_tools/ https://bahanonu.com/syscarut/articles/233/ Notes: I use cell extraction to refer to algorithms that perform cell segmentation and extract neural activity traces. In cases where the publication did not explicitly give the algorithm a name, made one based on the underlying method used. This table includes algorithms that simultaneously extract cell images/contours and reconstruct cell activity traces along with ones mainly focused on determining one or the other. Several calcium imaging related packages have also been included along with algorithms dealing with post-hoc handling of data or cell activity traces. Future versions of the repository will include table file (e.g. CSV) and basic LaTeX code so others can import or modify the table more easily going forward. Depending on monitor size and browser, scroll horizontally to see right-most table columns (e.g. websites/URLs). Any additional papers or algorithms that should be added or suggested updates to the table, leave a comment on the associated blog post or open an issue on the GitHub page, I want to make sure everyone’s brilliant work is acknowledged! An example calcium imaging analysis pipeline: CIAtah (https://github.com/bahanonu/ciatah).

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