Imaging Python Packages

multiscale-spatial-image

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

itkwasm

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

ngff-zarr

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

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

itkwidgets

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

atomai

Deep and Machine Learning for Microscopy

pyabel

A python package for Abel and inverse Abel transforms

deepinv

DeepInverse: a PyTorch library for solving imaging inverse problems using deep learning

cellfinder

Automated 3D cell detection in very large images

odl

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

suite2p

cell detection in calcium imaging recordings

cp-measure

Morphological features from images and masks made easy.

fileglancer

Browse, share, and publish OME-Zarr data

itkwasm-image-io

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

itkwasm-image-io-wasi

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

simtk

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

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.

starfish

starfish: unified pipelines for image-based transcriptomics

itk-ioscanco

ITK Image IO for Scanco MicroCT .ISQ files

bidscoin

BIDScoin converts your source-level neuroimaging data to BIDS

itk-webassemblyinterface

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

torchoptics

Differentiable wave optics simulation library built on PyTorch

itkwasm-compare-images-wasi

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