glencoesoftware/bioformats2raw

Bio-Formats image file format to raw format converter

Language: Java - Size: 1.05 MB - Last synced at: 1 day ago - Pushed at: 2 days ago - Stars: 94 - Forks: 36

thewtex/ngff-zarr

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

Language: Python - Size: 7.42 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 46 - Forks: 10

spatial-image/multiscale-spatial-image

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

Language: Python - Size: 2.95 MB - Last synced at: 12 days ago - Pushed at: 6 months ago - Stars: 44 - Forks: 9

czbiohub-sf/iohub

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

Language: Python - Size: 718 KB - Last synced at: 4 days ago - Pushed at: 5 days ago - Stars: 38 - Forks: 10

scalableminds/webknossos-libs

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

Language: Python - Size: 217 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 25 - Forks: 13

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: Python - Size: 10.7 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 21 - Forks: 3

ome/ome2024-ngff-challenge

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

Language: Python - Size: 1.34 MB - Last synced at: 4 days ago - Pushed at: 2 months ago - Stars: 19 - Forks: 16

fractal-analytics-platform/fractal-tasks-core

Main tasks for the Fractal analytics platform

Language: Python - Size: 10.3 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 17 - Forks: 7

saalfeldlab/n5-ij

ImageJ convenience layer for N5

Language: Java - Size: 2.75 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 17 - Forks: 12

ome/omero-cli-zarr

Language: Python - Size: 369 KB - Last synced at: 5 days ago - Pushed at: 12 days ago - Stars: 17 - Forks: 10

fmi-faim/faim-ipa

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

Language: Python - Size: 70.4 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 17 - Forks: 8

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.

Language: Python - Size: 2.87 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 11 - Forks: 1

InsightSoftwareConsortium/ITKIOOMEZarrNGFF

ITK IO for images stored in OME-Zarr format.

Language: C++ - Size: 151 KB - Last synced at: 11 days ago - Pushed at: 9 months ago - Stars: 10 - Forks: 5

FrancisCrickInstitute/OmeSliCC

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

Language: Python - Size: 1.67 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 7 - Forks: 1

BodenmillerGroup/mcd2zarr

Command line tool to convert MCD files to Zarr

Language: Python - Size: 14.6 KB - Last synced at: 9 days ago - Pushed at: 10 days ago - Stars: 2 - Forks: 1

BioVisionCenter/ome-zarr-converters-tools

Tooling to build ome-zarr plate converters

Language: Python - Size: 26.1 MB - Last synced at: 3 days ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 2

leukemia-kispi/operetta-compose

Fractal tasks for the Opera/Operetta microscope and drug profiling

Language: Python - Size: 7.17 MB - Last synced at: 16 days ago - Pushed at: 19 days ago - Stars: 1 - Forks: 1

fractal-analytics-platform/fractal-plantseg-tasks

A collection of fractal tasks to run plantseg workflows

Language: Python - Size: 2.18 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 2

JaneliaSciComp/nf-omezarr

Nextflow pipeline for converting images to OME-Zarr using bioformats2raw

Language: Groovy - Size: 1.91 MB - Last synced at: about 2 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0

fractal-analytics-platform/fractal-uzh-converters

A collection of fractal tasks to convert HCS Plates to OME-Zarr

Language: Python - Size: 7.56 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

lorenzocerrone/fractal-hcs-drogon-converters

Simple converter from the drogon plate format to OME-Zarr

Language: Python - Size: 1.91 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 1

fractal-analytics-platform/fractal-lif-converters

Converter from the Lif files (Leica Microscope) to OME-Zarr format.

Language: Python - Size: 3.92 MB - Last synced at: 15 days ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0