Pinned Repositories
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.
Galaxy-OME-Zarr
Integration of certain OME-Zarr tools in Galaxy.
image_processing
A repo with several common tools for 3D image processing
Next-Generation-File-Format-Features
This repository is a proposal for addin generalistic feature specs in the context of the next generation bioimage analysis workflows hackathon 2023
ome_zarr_pyramid
OME_Zarr_Tools
Course materials for the practical on the Defragmentation Training School 2 - Porto, 8-12 May 2023
PatternFileGenerator
Tool to generate a pattern file under the name "new.pattern", which can be used by bioformats to concatenate multiple files into a hyperstack.
PythonImageConverters
A module that runs the image data converters bfconvert and bioformats2raw from python using the subprocess module..
Rclone-BIA
Scripts to facilitate exchange of data between local filesystems and BioImage Archive
ZarrSeg
Command line tool to segment local and remote OME-Zarr data
Euro-BioImaging ERIC's Repositories
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.
Euro-BioImaging/ome_zarr_pyramid
Euro-BioImaging/OME_Zarr_Tools
Course materials for the practical on the Defragmentation Training School 2 - Porto, 8-12 May 2023
Euro-BioImaging/image_processing
A repo with several common tools for 3D image processing
Euro-BioImaging/ZarrSeg
Command line tool to segment local and remote OME-Zarr data
Euro-BioImaging/galaxy-image-analysis
Galaxy tools for image analysis
Euro-BioImaging/Galaxy-OME-Zarr
Integration of certain OME-Zarr tools in Galaxy.
Euro-BioImaging/Next-Generation-File-Format-Features
This repository is a proposal for addin generalistic feature specs in the context of the next generation bioimage analysis workflows hackathon 2023
Euro-BioImaging/PatternFileGenerator
Tool to generate a pattern file under the name "new.pattern", which can be used by bioformats to concatenate multiple files into a hyperstack.
Euro-BioImaging/PythonImageConverters
A module that runs the image data converters bfconvert and bioformats2raw from python using the subprocess module..
Euro-BioImaging/Rclone-BIA
Scripts to facilitate exchange of data between local filesystems and BioImage Archive
Euro-BioImaging/Data
Example data that can be used to test tools.
Euro-BioImaging/centriole_tracking_preprocess
Euro-BioImaging/convert_and_concatenate
Euro-BioImaging/ngff
Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.