Table of imaging analysis methods and software

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).