Calcium Imaging Python Packages

mesc-io

Read Femtonics .mesc two-photon recordings, in the units the native reader shows

isx

Python API for interacting with Inscopix data.

cindra

Provides pipelines for processing neural imaging data and tracking Regions of Interest across multiple recordings.

vineseg

"ViNe-Seg: A deep-learning tool for semi-automatic neural soma segmentation and subsequent analysis in a user-friendly interface"

mio

miniscope I/O sdk

optinist

calcium imaging pipeline tool

derotation

Derotate images acquired via multiphoton calcium imaging

mesmerize

Platform for Calcium Imaging analysis. DEPRECATED.

mesmerize-core

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

stiminterp

Remove photostimulation artefacts from images acquired via multiphoton calcium imaging

photon-mosaic

Automated and reproducible analysis of multiphoton imaging datasets

hnccorr

HNCcorr algorithm for neuron identification in calcium imaging datasets.

photon-mosaic-pipeline

Automated and reproducible analysis of multiphoton imaging datasets

fipster

Build your own camera-based multi-fiber and multi-color fiber photometry (FIP) system!

lbm-mc

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

neuroglia

a Python machine learning library for neurophysiology data

samuroi

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