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spatial-image
multiscale-spatial-image

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

82K 55 9
thewtex
ngff-zarr

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

27K 69 18
scalableminds
cluster-tools

Python API and CLI tools for working with WEBKNOSSOS datasets, annotations and server interactions. Includes converter to OME-Zarr.

15K 28 14
scalableminds
webknossos

Python API and CLI tools for working with WEBKNOSSOS datasets, annotations and server interactions. Includes converter to OME-Zarr.

13K 28 14
fractal-analytics-platform
fractal-tasks-core

Main tasks for the Fractal analytics platform

11K 25 8
czbiohub-sf
iohub

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

10K 52 13
Euro-BioImaging
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.

3K 27 1
InsightSoftwareConsortium
itk-ioomezarrngff

ITK IO for images stored in OME-Zarr format.

2K 11 5
ome
omero-cli-zarr

Plugin for exporting images in zarr format.

2K 20 11
BioVisionCenter
ome-zarr-converters-tools

Tooling to build ome-zarr HCS plate converters

2K 6 5
fmi-faim
faim-ipa

Tools used at FMI-FAIM for Image Processing and Analysis.

1K 20 9
fractal-analytics-platform
fractal-converters-tools

Tooling to build ome-zarr HCS plate converters

514 6 5
leukemia-kispi
operetta-compose

Fractal tasks for the Opera/Operetta microscope and drug profiling

485 1 2
spatial-image
spatial-image-multiscale

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

440 55 9
FrancisCrickInstitute
omeslicc

Ome(ro) SLide Image Conversion and Compression pipline (OmeSliCC)

382 7 1
thewtex
ngff-zarr-mcp

Model Context Protocol server for OME-Zarr image conversion

313 69 18
ome
ome2024-ngff-challenge

Tools for converting OME-Zarr data within the ome2024-ngff-challenge (see https://forum.image.sc/t/ome2024-ngff-challenge/97363)

270 21 20
BodenmillerGroup
mcd2zarr

Command line tool to convert MCD files to Zarr

70 2 1
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