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two-photon-alignment

Version 2 has now been pushed to master!

Version 1 is available in the branch version1_stable in case it is needed.

Features in version 2: (all complete unless otherwise noted)

  1. Load multiple F_proc.mat files generated by suite2p, and data files made by included CaImAn exporter. Some F_proc.mat files from older versions of Suite2P and unclassified F*.mat files from Suite2P are supported. Not all possible variations have been tested, so specific versions should be tested individually and may require addition of a case-specific parser.
  2. Display ROIs generated by suite2p superimposed on mean image.
  3. Select ROIs with mouse click and view details of ROI and trace on labelled time axis.
  4. Label ROIs selected in two data sets as representing the same cell.
  5. Generate Transform and align mean images between two datasets - two automatic and two manual options for generating transform.
  6. Transform ROIs into reference session mean image frame of reference, and automatically identify ROIs that match. Match can be determined either by the distance between center points or by the percentage overlap of the reference ROI with the transformed ROI from the selected session.
  7. Transplant transformed ROIs between sessions.
  8. Combine ROIs within a dataset to make a single ROI, and delete unwanted ROIs. This should be done before matching ROIs between sessions.
  9. Export sets of ROIs including additions, sorted so that ROI numbers match between sessions.
  10. Save modified data structure for future manipulation.
  11. Output modified & matched ROIs, or Qmatrix including all ROIs aligned to reference session. Other output formats can be added as needed.
  12. Display and sort by several parameters such as ROI aspect ratio, trace skew (supported for some input file types), match type between ROIs from different sessions, ROI size.

Features for later version:

  1. Concurrently access registered image data for ROI modification.
  2. Additional support viewing ROIs against representative images such as skew and 95th percentile in addition to mean image. Currently new background images can be loaded, but loading requires user to write a function to pass back the mimg stack.

Example workflow

Sample data for testing is courtesy of Zaneta Navratilova, and is an interesting set due to the presence of many dendrites.