Imaging Python Packages

multiscale-spatial-image

Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.

ngff-zarr

A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.

itkwasm

High performance spatial analysis in a web browser and across programming languages and hardware architectures

itkwasm-downsample

High performance spatial analysis in a web browser and across programming languages and hardware architectures

itkwasm-downsample-wasi

High performance spatial analysis in a web browser and across programming languages and hardware architectures

starfish

starfish: unified pipelines for image-based transcriptomics

itkwidgets

An elegant Python interface for visualization on the web platform to interactively generate insights into multidimensional images, point sets, and geometry.

pyabel

A python package for Abel and inverse Abel transforms

fileglancer

Browse, share, and publish OME-Zarr data

suite2p

cell detection in calcium imaging recordings

cellfinder

Automated 3D cell detection in very large images

cp-measure

Morphological features from images and masks made easy.

itkwasm-image-io-wasi

High performance spatial analysis in a web browser and across programming languages and hardware architectures

neunorm

Neutron Imaging Loading and Normalization Tools

itkwasm-image-io

High performance spatial analysis in a web browser and across programming languages and hardware architectures

odl

Operator Discretization Library https://odl.readthedocs.io/

glam-radiomics

Gray Level Affinity Metrics (GLAM)

nereids

NEREIDS (NEutron REsonance Imaging Diagnostic Suite) is a research-grade toolkit for neutron resonance imaging, providing a Rust physics core, Python bindings, and NeXus/HDF5-compliant data I/O, with a path to fast, standalone GUI workflows for VENUS/MARS.

atomai

Deep and Machine Learning for Microscopy

bidscoin

BIDScoin converts your source-level neuroimaging data to BIDS

itk-ioscanco

ITK Image IO for Scanco MicroCT .ISQ files

itk-ioomezarrngff

ITK IO for images stored in OME-Zarr format.

simtk

Place to build a Python version of the SIM reconstruction code.

ngff-zarr-mcp

A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.