A collection of fractal tasks to run plantseg workflows
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Updated
Sep 17, 2024 - Python
A collection of fractal tasks to run plantseg workflows
Converter from the Lif files (Leica Microscope) to OME-Zarr format.
Fractal tasks for the Opera/Operetta microscope and drug profiling
Run encapsulated docker containers with BioFormats2Raw in the Amazon Web Services infrastructure.
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
Ome(ro) SLide Image Conversion and Compression pipline (OmeSliCC)
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.
Project planning and material repository for the 2024 challenge to generate 1 PB of OME-Zarr data
Main tasks for the Fractal analytics platform
ImageJ convenience layer for N5
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.
A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.
Python API and CLI tools for working with WEBKNOSSOS datasets, annotations and server interactions. Includes converter to OME-Zarr.
Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata
Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.
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