Calcium Imaging Python Packages

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

Image Polygonal Annotation with Python

stiminterp

Remove photostimulation artefacts from images acquired via multiphoton calcium imaging

derotation

Derotate images acquired via multiphoton calcium imaging

photon-mosaic-pipeline

Automated and reproducible analysis of multiphoton imaging datasets

mio

miniscope I/O sdk

optinist

Calcium Imaging Pipeline Tool

mesmerize

Platform for Calcium Imaging analysis. DEPRECATED.

photon-mosaic

Automated and reproducible analysis of multiphoton imaging datasets

mesmerize-core

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

hnccorr

HNCcorr algorithm for cell detection in calcium-imaging.

lbm-mc

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

fipster

Fiber photometry analysis tools used by Fipster.

neuroglia

scikit-learn compatible transformers for neural data science

samuroi

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

lcp-mc

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