python Signal Extraction And Segmentation (pySEAS)

This is a python package for ICA signal extraction and segmentation of mesoscale calcium imaging videos.

Publication

Weiser SC, Mullen BR, Ascencio D, Ackman JB (2023) Data-driven segmentation of cortical calcium dynamics. PLOS Computational Biology 19(5): e1011085. article link.

Installation

pip install seas

Please see the install-notes for further troubleshooting details, and report any bugs you find to our Github issues page.

Test Data

Test ica processed datasets are available for download from Dryad.

Contents

• seas package
  • seas.colormaps module
  • seas.defaults module
  • seas.domains module
  • seas.experiment module
  • seas.filemanager module
  • seas.gui module
  • seas.hdf5manager module
  • seas.ica module
  • seas.rois module
  • seas.signalanalysis module
  • seas.video module
  • seas.waveletAnalysis module
  • seas.waveletFunctions module
• Example Usage
  • Play dFoF Movie
  • ICA Project
  • View Components
  • Domain Map
  • HDF5 Manager
• Installation Notes
  • AV Libraries
  • Virtual Environments
  • Tkinter