A simple and performant native R reader & writer for Zarr Arrays

ngio is a Python library to streamline OME-Zarr image analysis workflows.

Repository of scripts to facilitate participation in CellMap's segmentation challenge. This includes downloading data, simple setups for training 2D and 3D models, workflows for prediction and post-processing on out-of-memory arrays, and evaluation of results against validation data.

Browse, share, and publish OME-Zarr data

A web-based resource for the scientific visualization community to enhance reproducibility and facilitate testing and development of OME-Zarr tools.

Project planning and material repository for the 2024 challenge to generate 1 PB of OME-Zarr data

A Rust library for OME-Zarr (previously OME-NGFF) metadata

Tooling to build ome-zarr plate converters

Advanced methods in bioimage analysis

This repository is a proposal for addin generalistic feature specs in the context of the next generation bioimage analysis workflows hackathon 2023

Clear multiscale image metadata manipulation in python

A collection of Fractal tasks to convert from several microscopes into OME-Zarr format.

Browser-based OME-ZARR microscopy viewer. Open local files, annotate, overlay segmentation labels, share deep links. GPU-accelerated, privacy-first, zero-install.

Native desktop viewer for large 4D microscopy datasets (pre-alpha).

Scientific AI and the Future of OME-NGFF: Intelligent Bioimage Analysis Workflows

Python GUI microscopy file converter for ICS2, IMS, LIF, ND2, ZVI, TIFF, OME-TIFF and OME-Zarr bioimaging datasets.

OME-Zarr whole-slide images to patch- and slide-level foundation-model embeddings - cloud-native, FAIR, model- and backend-agnostic.

Present TIFF files as a zarrita.js Zarr store following the NGFF OME-Zarr data model

Simple converter from the drogon plate format to OME-Zarr

A collection of Fractal tasks to convert Zeiss .czi files into OME-Zarr format.