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.

ROI

Stands for Region Of Interest, which is the set of pixels from acquired fluorescence images which the segmentation software has determined to follow a particular cellular structure.

With this package, a user can:

  • Work with imaging data in formats like: ScanImage TIFF, HDF5, Miniscope, Scanbox and more.

  • 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.

  • Leverage a common API to streamline analysis and visualization of data from different acquisition systems and cell extraction/segmentation pipelines.

See also

If you want to write data to NWB, you can check out our primary dependent: NeuroConv.