Spatial omics in the browser for hundreds of images at once | 10x, IMC, IF, H&E, CosMX, & more | https://rakaia.io/

napari: a fast, interactive, multi-dimensional image viewer for python

Native Zarr 3 Support for R

A multiscale cellular architecture visualization toolkit.

Piecewise alignment for layers of mosaics

utitilies for macsima image sets

Interactive Vitessce visualizations for Harpy workflows. https://harpy-vitessce.readthedocs.io/en/latest/

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

Multi-Dimensional Visualization (MDV) is an open-source toolkit for analyzing and visualizing spatial and molecular datasets. Code licensed under GPL-3.0; example spatial data under CC0 1.0.

OMERO Process Container Steward

work in progress for a new intermediate image analysis training workshop

Open Source Computer Vision Library

N-dimensional image registrations

An introduction to bioimage analysis - http://bioimagebook.github.io

Python tools for geographic data

NL‑BIOMERO delivers a full containerized stack to run OMERO together with the BIOMERO 2.0 framework. It provides Docker/Podman configurations and Compose files to deploy OMERO + BIOMERO subsystems …

High-level DICOM abstractions for the Python programming language

NGFF-Converter is a GUI application for conversion of bioimage formats into OME-NGFF (Next-Generation File Format) or OME-TIFF

An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.

Book repository for The Turing Way: a how to guide for reproducible, ethical and collaborative data science

Experimental micro-service for implementing the Zarr spec over HTTP

Dataframe-agnostic Zarr Storage powered by Narwhals

DenoIST: Denoising Image-based Spatial Transcriptomics data

OMERO plugin for metadata manipulation https://www.openmicroscopy.org/omero/

Domain-agnostic Zarr convention for encoding multiscale pyramid information