ome-zarr-converter

There are 20 repositories under ome-zarr-converter topic.

glencoesoftware/bioformats2raw
Bio-Formats image file format to raw format converter
Language:Java84 18 9335
spatial-image/multiscale-spatial-image
Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.
Language:Python38 6 368
czbiohub-sf/iohub
Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata
Language:Python32 5 1268
scalableminds/webknossos-libs
Python API and CLI tools for working with WEBKNOSSOS datasets, annotations and server interactions. Includes converter to OME-Zarr.
Language:Python23 9 40312
thewtex/ngff-zarr
A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.
Language:Python23 4 384
Euro-BioImaging/BatchConvert
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.
Language:Python20 3 142
ome/ome2024-ngff-challenge
Project planning and material repository for the 2024 challenge to generate 1 PB of OME-Zarr data
Language:Python16 16 2214
ome/omero-cli-zarr
Language:Python16 9 2510
saalfeldlab/n5-ij
ImageJ convenience layer for N5
Language:Java16 11 6012
fractal-analytics-platform/fractal-tasks-core
Main tasks for the Fractal analytics platform
Language:Python14 4 5336
InsightSoftwareConsortium/ITKIOOMEZarrNGFF
ITK IO for images stored in OME-Zarr format.
Language:C++10 5 335
fmi-faim/faim-ipa
A collection of Image Processing and Analysis (IPA) functions used at the Facility for Advanced Imaging and Microscopy (FAIM)
Language:Python9 4 886
FrancisCrickInstitute/OmeSliCC
Ome(ro) SLide Image Conversion and Compression pipline (OmeSliCC)
Language:Python7 7 01
BioinfoTongLI/to_ome_tif
nextflow DSL2 pipeline (leveraging ![bioformats2raw](https://github.com/glencoesoftware/bioformats2raw)/[raw2ometiff](https://github.com/glencoesoftware/raw2ometiff)) to convert almost any images to ome.tiff/ome.zarr
Language:Nextflow4 1 00
DistributedScience/Distributed-OMEZarrCreator
Run encapsulated docker containers with BioFormats2Raw in the Amazon Web Services infrastructure.
Language:Python3 3 51
BodenmillerGroup/mcd2zarr
Command line tool to convert MCD files to Zarr
Language:Python2 4 21
JaneliaSciComp/nf-omezarr
Nextflow pipeline for converting images to OME-Zarr using bioformats2raw
Language:Groovy1 4 0
leukemia-kispi/operetta-compose
Fractal tasks for the Opera/Operetta microscope and drug profiling
Language:Python0 1 81
fractal-analytics-platform/fractal-lif-converters
Converter from the Lif files (Leica Microscope) to OME-Zarr format.
Language:Python2 1
fractal-analytics-platform/fractal-plantseg-tasks
A collection of fractal tasks to run plantseg workflows
Language:Python

ome-zarr-converter

glencoesoftware/bioformats2raw

spatial-image/multiscale-spatial-image

czbiohub-sf/iohub

scalableminds/webknossos-libs

thewtex/ngff-zarr

Euro-BioImaging/BatchConvert

ome/ome2024-ngff-challenge

ome/omero-cli-zarr

saalfeldlab/n5-ij

fractal-analytics-platform/fractal-tasks-core

InsightSoftwareConsortium/ITKIOOMEZarrNGFF

fmi-faim/faim-ipa

FrancisCrickInstitute/OmeSliCC

BioinfoTongLI/to_ome_tif

DistributedScience/Distributed-OMEZarrCreator

BodenmillerGroup/mcd2zarr

JaneliaSciComp/nf-omezarr

leukemia-kispi/operetta-compose

fractal-analytics-platform/fractal-lif-converters

fractal-analytics-platform/fractal-plantseg-tasks