Python API and CLI tools for working with WEBKNOSSOS datasets, annotations and server interactions. Includes converter to OME-Zarr.
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Updated
Jul 9, 2024 - Python
Python API and CLI tools for working with WEBKNOSSOS datasets, annotations and server interactions. Includes converter to OME-Zarr.
A collection of Image Processing and Analysis (IPA) functions used at the Facility for Advanced Imaging and Microscopy (FAIM)
Fractal tasks for the Opera/Operetta microscope and drug profiling
Main tasks for the Fractal analytics platform
Ome(ro) SLide Image Conversion and Compression pipline (OmeSliCC)
ITK IO for images stored in OME-Zarr format.
ImageJ convenience layer for N5
A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.
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.
Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.
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
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