Imaging analysis methods and code

Outline of outside code, software packages, or techniques relevant to calcium imaging analysis. Also includes links to papers or GitHub code repositories.

Find an overview of calcium imaging analysis methods at https://bahanonu.com/brain/#c20181209. Or see below. image

Image Registration

Cross-day alignment

Cell segmentation (static image)

Cell extraction (dynamic movie)

  • Seeds Cleansing CNMF for Spatiotemporal Neural Signals Extraction of Miniscope Imaging Data (Simon email this one out recently)

Cell-extraction correction

Full packages

Standards