Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.

Complete Matlab pipeline for large scale calcium imaging data analysis

Matlab routines for online non-rigid motion correction of calcium imaging data

Calibrated inference of spiking from calcium ΔF/F data using deep networks

CIAtah (pronounced cheetah): a software package for calcium imaging analysis of one- and two-photon imaging datasets. Documentation: https://git.io/ciatah_docs. Formerly known as calciumImagingAnalysis (ciapkg).

High level pandas-based API for batch analysis of Calcium Imaging data using CaImAn

Accurate denoising of voltage imaging data through statistically unbiased prediction, Nature Methods.

calcium imaging pipeline tool

Platform for Calcium Imaging analysis. DEPRECATED.

The Zebrafish Activity Prediction Benchmark measures progress on the problem of predicting cellular-resolution neural activity throughout an entire vertebrate brain.

utility functions for analyzing (fly) calcium imaging data

Fast, Simple Calcium Imaging Segmentation with Fully Convolutional Networks (https://arxiv.org/abs/1707.06314)

a Python machine learning library for neurophysiology data

Seeded Iterative Demixing (SID) of neuronal activity recordings made using Light Field Microscopy (LFM)

SamuROI - Structured analysis of multiple user-defined ROIs, an open source Python-based analysis environment for imaging data.

Code and tutorials for fitting generalized linear models (GLM) in Tensorflow 2

Bonsai package for controlling headborne, calcium imaging miniscopes

Official code for BEAR. "Efficient neural network approximation of robust PCA for automated analysis of calcium imaging data", MICCAI 2021.

Flow-Registration toolbox for 2P motion compensation

Analysis and characterisation of cells within the gut wall using deep learning models. The current focus is on studying enteric neurons and enteric glia.