Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
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Updated
Feb 19, 2026 - Python
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.
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
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.
Automated and reproducible analysis of multiphoton imaging datasets
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.
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