Welcome to RoiExtractors’s documentation!

Roiextractors is a library that helps in analyzing, visualizing and interacting with optical physiology data acquired from various acquisition systems.


Stands for Region Of Interest, which is the region in a set of acquired fluorescence images which the segmentation software has determined as a neuron.

With this package, a user can:

  • Work with imaging data in formats like: TIFF, HDF5, STK, FLI.

  • Work with post-processed data (after application of cell extraction/segmentation) output from various commonly used cell extraction/segmentation packages like Suite2p, CNMF-E, Caiman, SIMA.

  • Save all this data into NWB format and share it with the community!

Indices and tables