Ome Zarr Python Packages

ome-zarr

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

ome-zarr-models

A minimal Python package for reading, writing and validating OME-Zarr (meta)data

ngff-zarr

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

pymmcore-plus

Pure python/C++ micro-manager ecosystem

iohub

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

fractal-tasks-core

Main tasks for the Fractal analytics platform

ngio

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

fileglancer

Browse, share, and publish OME-Zarr data

multiview-stitcher

A Python toolbox for aligning / fusing / stitching large multi-view / multi-positioning image datasets in 2-3D.

ome-zarr-converters-tools

Tooling to build ome-zarr plate converters

ome-writers

Unified API for streaming camera frames to either OME-TIFF or OME-Zarr format

eubi-bridge

A Python-based tool for parallelized conversion of image datasets from various formats to OME-Zarr, with support for distributed processing and multi-dimensional concatenation.

zarrnii

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

itk-ioomezarrngff

ITK IO for images stored in OME-Zarr format.

faim-ipa

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

ngff-zarr-mcp

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

ez-zarr

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

operetta-compose

Fractal tasks for the Opera/Operetta microscope and drug response profiling

fractal-converters-tools

Tooling to build ome-zarr plate converters

ome-zarrpari

Load OME-Zarr data into napari

raw2features

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

anu-ctlab-qemscan-bse-to-zarr3

Convert QEMSCAN data to a Zarr V3 image pyramid with OME-Zarr metadata

zarrnii-plugin-api

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