neuralib.imaging.spikes.oasis

oasis_dcnv	Computes non-negative deconvolution (no sparsity constraints)
oasis_matrix	Performs spike deconvolution for a single neuron's calcium imaging trace using a greedy method

OASIS

Fast online deconvolution of calcium imaging dat

Method source

• https://github.com/j-friedrich/OASIS

• https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005423

This script adapted from suite2p.suite2p.extraction.dcnv (Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu)

See also

https://github.com/MouseLand/suite2p/blob/main/suite2p/extraction/dcnv.py

Example of usage

from neuralib.imaging.spikes.oasis import oasis_dcnv

# 2D dF/F array. Array[float, [nNeurons, nFrames]] or Array[float, nFrames]
dff = ...

tau = 1.5  # time constant of the calcium indicator (ms)
fs = 30  # sampling frequency of the calcium imaging data (hz)
spks = oasis_dcnv(dff, tau, fs)