Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.

A simple native R reader for Zarr Arrays

Pure python/C++ micro-manager ecosystem

Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata

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

A nextflow based tool that wraps bfconvert and bioformats2raw to convert image data collections to OME-TIFF and OME-Zarr, respectively, in a parallelised manner.

Various tools for creating and manipulating Zarr v3 data with the zarrs rust crate

Main tasks for the Fractal analytics platform

GIve easy, high-level access to ome-zarr fileset

Create web-based OME-Zarr galleries

A collection of Image Processing and Analysis (IPA) functions used at the Facility for Advanced Imaging and Microscopy (FAIM)

ITK IO for images stored in OME-Zarr format.

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

Advanced methods in bioimage analysis

Web page for validating OME-NGFF files

Large-scale cell segmentation with cellpose.

Run encapsulated docker containers with BioFormats2Raw in the Amazon Web Services infrastructure.

Course materials for the practical on the Defragmentation Training School 2 - Porto, 8-12 May 2023

Document available viewers and other tools for the OME-NGFF image format

Package for working with OME-Zarr and NIFTI images in a unified manner, with a focus on spatial transformations