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Extraction

This capsule combines cellpose and suite2p to perform cell detection and signal extraction.

Input

All parameters are passed to extraction.py using python extraction.py [parameters]. All parameters are defined in main using argparse. The most important one is 'input-dir' which should point to a directory that includes an hdf5 file with a 'data' 3D array of the registered (or, in the case of multi-plane imaging, decrosstalked) movie.

Output

The main output is the extraction.h5 file.
For QC, the figures detected_ROIs.png and detected_ROIs_withIDs.png display contours of the detected ROIs over a selection of summary images. If the capsule is run with the --contour_video argument, a 10x sped-up video is also created, showing ROI contours overlaid on the raw data, along with ROI activity and the remainder.
The extraction.h5 file contains three groups: traces, rois, and cellpose, with the latter only present if Cellpose is used for detection (--anatomical_only ≠ 0).

traces:

  • corrected: Neuropil-corrected fluorescence traces
  • roi: Neuropil-corrupted raw fluorescence traces of each ROI
  • neuropil: Neuropil fluorescence traces
  • neuropil_rcoef: Coefficients used for neuropil correction
  • raw_neuropil_rcoef_mutualinfo: Raw coefficients for neuropil correction (minimizing mutual information between corrected and neuropil trace)
  • skew: Skewness of neuropil-corrected fluorescence traces
  • std: Standard deviation of neuropil-corrected fluorescence traces

rois:

  • data: Values of the (weighted) ROIs
  • coords: Index locations of every data value
  • shape: Shape of the ROI array, # neurons x height of FOV (in pixels) x width of FOV (in pixels)
  • neuropil_coords: Index locations of neuropil masks
  • aspect_ratio, compact, footprint, med, mrs, mrs0, npix, npix_norm, npix_norm_no_crop, npix_soma, overlap, radius, solidity, soma_crop: Additional ROI stats, see suite2p documentation

cellpose:

  • masks: Labeled image, where 0=no masks; 1,2,…=mask labels.
  • flows_in_hsv: XY flow in HSV 0-255
  • flows: XY flows at each pixel
  • cellprob: Cell probability at each pixel
  • final_locations: Final pixel locations after Euler integration
  • styles: Style vector summarizing each image

Additional datasets at the root of extraction.h5 are:

  • iscell: Specifies whether a ROI is a cell, first column is 0/1, and second column is probability that the ROI is a cell based on the default classifier
  • meanImg: The mean image of the movie over time
  • maxImg: The maximum intensity projection of the movie over time