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

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

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

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

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

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

Platform for Calcium Imaging analysis. DEPRECATED.

A table containing imaging analysis tools for biology, with a focus on calcium imaging.

calcium imaging pipeline tool

a Python machine learning library for neurophysiology data

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

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

Flow-Registration toolbox for 2P motion compensation

Automated and reproducible analysis of multiphoton imaging datasets

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

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

Derotate images acquired via multiphoton calcium imaging

This repository contains code for morphology-free analysis of functional fluorescence microscopy. The focal algorithm, Graph-Filtered Time-trace (GraFT) Dictionary Learning, is published in Charles et al. 2022 in the IEEE Transactions of Image Processing.

Real-time, interactive exploration of 3D image stacks

Bonsai package for controlling headborne, calcium imaging miniscopes

HNCcorr algorithm for neuron identification in calcium imaging datasets.

Python API for interacting with Inscopix data.

Codes related to paper "Automated sleep stage classification of wide-field calcium imaging data via multiplex visibility graphs and deep learning"

miniscope I/O sdk

Custom code (Python or Matlab) to compute centripetal propagation from astrocytic calcium recordings using pixel-wise correlation functions

Preserving Spatial and Quantitative Information in Unpaired Biomedical Image-to-Image Translation

a Python toolbox for reproducible analysis and visualization of NeuroPhysiological data.

Signal Processing Toolbox for Calcium Imaging Data