Suite2p

Suite2p is a pipeline for processing two-photon calcium imaging data. It handles motion correction, ROI (cell) detection, fluorescence extraction, neuropil subtraction, and spike deconvolution.

Input formats

.tiff, .h5, .hdf5, .sbx, .nd2, .raw

Parameters

Parameter	Range	Default	Description
nplanes	1–100	1	Number of imaging planes
nchannels	1–4	1	Number of channels
Functional channel	1–4	1	Channel to use for cell detection
Frame rate	Float	Auto-detected	Imaging frame rate (Hz)
Motion correction	rigid / non-rigid	rigid	Type of motion correction
Block size	[Int, Int]	[128, 128]	Block size for non-rigid correction
Gaussian smoothing	Float	0	Smoothing sigma for cell detection
Cell diameter	Integer	0 (auto)	Expected cell diameter in pixels
Detection threshold	0.1–5	1.0	Scaling factor for detection sensitivity
Sparse mode	Toggle	Off	Better for sparse recordings
Overlapping ROIs	Toggle	Off	Allow ROIs to overlap
Spike deconvolution	Toggle	On	Deconvolve calcium transients to spikes
Indicator tau	0.1–10	1.0	Calcium indicator time constant (seconds)
MATLAB export	Toggle	Off	Export results in MATLAB format
Combined planes	Toggle	Off	Combine ROIs across planes

Outputs

Output	Format	Description
Cell statistics	NPY	ROI shapes, positions, and properties
ROI map	NPY	Spatial footprints of detected cells
Raw fluorescence (F)	NPY	Raw fluorescence traces per cell
Neuropil (Fneu)	NPY	Neuropil contamination traces
Deconvolved spikes	NPY	Estimated spike trains
Cell classification	NPY	Classifier labels (cell vs. not-cell)
Registered movie	BIN	Motion-corrected movie (optional)

Presets

Preset	Description
Default	Standard settings for most recordings
Fast Processing	Reduced accuracy for quick preview
Multi-plane	Configured for multi-plane imaging
Dense Labeling	Lower threshold for densely labeled samples

Compute requirements

Resource	Requirement
GPU	A10G or A100 for large datasets (8–14+ GB VRAM)
Duration	~600 seconds baseline

DeepLabCut — Pose Estimation

SpikeInterface — Spike Sorting