suite2p output conversion¶

This tool uses 2.0 compute credits per hour.

Overview¶

This suite2p output conversion tool is a wrapper for the suite2p functions io.save_nwb() and io.save_mat(), as well as for zipping the .npy output files and using the npy_to_isxd() function from our ideas-toolbox-suite2p package.
You can find more information on this processing step in the suite2p docs.

suite2p output conversion saves the neuropil-corrected fluorescence traces, neuropil fluorescence traces, deconvolved spikes, extraction statistics, classification labels and parameters information as 4 different formats: .zip containing suite2p's .npy outputs, .isxd cellset and eventset, .nwb and .mat.
Note that this tool constitutes the first step of Run suite2p pipeline.

Input files¶

Source Parameter	File Type	File Format
Fluorescence Traces File	suite2p_data	npy
Neuropil Fluo File	suite2p_data	npy
Deconvolved Spikes File	suite2p_data	npy
Extraction Statistics File	suite2p_data	npy
Parameters File	config	npy
Classification Labels File	suite2p_data	npy

Parameters¶

Parameter	suite2p name	Required?	Default	Description
Fluorescence Traces File	-	True	N/A	Input fluorescence traces file, as outputted by the ROI extraction step [.npy]
Neuropil Fluo File	-	True	N/A	Input neuropil fluorescence traces file, as outputted by the ROI extraction step [.npy]
Deconvolved Spikes File	-	True	N/A	Input deconvolved spikes file, as outputted by the spike deconvolution step [.npy]
Extraction Statistics File	-	True	N/A	Input extraction statistics file, as outputted by the ROI extraction step [.npy]
Parameters File	-	True	N/A	Input parameters file, as outputted by the spike deconvolution step [.npy]
Classification Labels File	-	True	N/A	Input classification labels file, as outputted by the ROI classification step [.npy]
Save NPY	-	False	True	If true, save suite2p NPY output (as a ZIP file) [bool]
Save ISXD	-	False	True	If true, save suite2p output as ISXD files [bool]
Save NWB	save_NWB	False	False	[from suite2p docs] "Whether to save output as NWB file." [bool]
Save MAT	save_mat	False	False	[from suite2p docs] "Whether to save the results in matlab format in file "Fall.mat"." [bool]
Spikes Percentile Threshold	-	False	99.7	Threshold for denoising the deconvolved spike trains, in percentile. Any value in the ROIs-by-time-point deconvolved spike matrix that is below the matrix's xth percentile value is set to 0. Note that the same threshold is applied to all ROIs, and that this thresholding step does not binarize the deconvolved spike trains but simply filters out the low-amplitude spike events [float, [0 100)]
FOV vmin Percentile	-	False	0	Minimum value for the colormap range, as percentile of the FOV fluorescence [float, [0 )]
FOV vmax Percentile	-	False	99	Maximum value for the colormap range, as percentile of the FOV fluorescence [float, ( 100]]
FOV Colormap	-	False	plasma	Colormap for plotting the FOV [str]
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
suite2p_output.zip	`.zip` file	Contains 6 `.npy` files outputted by in the previous steps: `F.npy`, `Fneu.npy`, `spks.npy`, `stat.npy`, `iscell.npy`, and `ops_spike_deconvolution.npy`.
cellset_raw.isxd	Inscopix `.isxd` file	Cell set containing the neuropil-corrected fluorescence traces for all extracted ROIs, as well as ROI footprints and classification labels.
eventset.isxd	Inscopix `.isxd` file	Event set containing the spike trains for all extracted ROIs.
ophys.nwb	`.nwb` file	Contains all the same output as `suite2p_output.zip` but in a `.nbw` format.
Fall.mat	`.mat` file	Contains all the same output as `suite2p_output.zip` but in a `.mat` format.

Each output file has metadata and previews attached to it.
For suite2p .zip, .nwb and .mat outputs, you can explore 8 preview figures, illustrating various aspects of the processing pipeline.
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):


Projection images from the registration process.	x and y offsets for both rigid and non-rigid registration.	Projection images and detected ROIs.
Accepted ROIs footprints.	Sample fluorescence traces, neuropil traces, and deconvolved spikes.	Footprints of the sample sources.
Raster plot of the deconvolved spikes.	Sample fluorescence traces, neuropil traces, and deconvolved spikes (suite2p* style).*

For Inscopix .isxd outputs, you can explore 2 preview figures for cellset_raw.isxd:


Sample fluorescence traces.	Footprints of the sample sources.

and 2 for eventset.isxd (also obtained from processing the same 5-minute 2P movie as above):


Sample fluorescence traces, neuropil traces, and deconvolved spikes.	Raster plot of the deconvolved spikes.