suite2p ROI extraction¶

This tool uses 2.0 compute credits per hour.

Overview¶

This suite2p ROI extraction tool is a wrapper for the suite2p function extraction.extraction_wrapper().
You can find more information on this processing step in the suite2p docs.

suite2p ROI extraction extracts neuropil-corrected fluorescence traces and corresponding neuropil fluorescence traces from the registered movie for all detected ROIs.
Note that this tool constitutes the fourth step of Run suite2p pipeline.

Input files¶

Source Parameter	File Type	File Format
Registered Binary Movie	suite2p_data	bin
Detection Statistics File	suite2p_data	npy
Parameters File	config	npy

Parameters¶

Parameter	suite2p name	Required?	Default	Description
Registered Binary Movie	-	True	N/A	Input registered suite2p binary movie [.bin]
Detection Statistics File	-	True	N/A	Input cell statistics file, as outputted by the ROI detection step [.npy]
Parameters File	-	True	N/A	Input suite2p parameters file, as outputted by the ROI detection tool [.npy]
Neuropil Extraction	neuropil_extract	False	True	[from suite2p docs] "Whether or not to extract signal from neuropil. If False, Fneu is set to zero." [bool]
Allow Overlap	allow_overlap	False	False	[from suite2p docs] "Whether or not to extract signals from pixels which belong to two ROIs. By default, any pixels which belong to two ROIs (overlapping pixels) are excluded from the computation of the ROI trace." [bool]
Minimum Neuropil Pixels	min_neuropil_pixels	False	350	[from suite2p docs] "Minimum number of pixels used to compute neuropil for each cell." [int, 0]
Inner Neuropil Radius	inner_neuropil_radius	False	2	[from suite2p docs] "Number of pixels to keep between ROI and neuropil donut." [int, =0]
Lambda Percentile	lam_percentile	False	50	[from suite2p docs] "Percentile of Lambda within area to ignore when excluding cell pixels for neuropil extraction." [int, [0 100]]
Show Grid on FOV	-	False	True	Whether or not to show the grid on FOVs [bool]
FOV Ticks Step	-	False	128	Step for the x- and y-ticks [int, >0]
Number of Sample Cells	-	False	20	Number of sample cells for the cell extraction preview [int, >0]
Random Seed	-	False	0	Random seed for selecting sample cells [int, >=0]
Show Non-Sample Cells' Footprints	-	False	True	Whether or not to show footprints of non-sample cells on the cell footprint FOV image. If False, only footprints of sample cells are displayed [bool]

Output files¶

File name	File type	Notes
stat.npy	NumPy file	Contains spatial and functional statistics for all extracted ROIs, as a dictionary.
F.npy	NumPy file	Contains neuropil-corrected fluorescence traces for all extracted ROIs, as a 2D array.
Fneu.npy	NumPy file	Contains neuropil fluorescence traces for all extracted ROIs, as a 2D array.
ops_ROI_extraction.npy	NumPy file	Contains a dictionary of parameters populated by `suite2p ROI extraction`.

You can explore 1 preview figures for stat.npy and 2 for F.npy.
You can find below an example of these previews obtained from processing a 5-minute 2P movie of mouse cortex (data courtesy of Dr. Ahmet Arac, MD, at UCLA).

For stat.npy:


Footprints of the sample sources.

and for F.npy:


Sample fluorescence traces.	Footprints of the sample sources.