Euro-BioImaging ERIC's 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.
OME_Zarr_Tools
Course materials for the practical on the Defragmentation Training School 2 - Porto, 8-12 May 2023
Galaxy-OME-Zarr
Integration of certain OME-Zarr tools in Galaxy.
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
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
galaxy-image-analysis
Galaxy tools for image analysis
image_processing
A repo with several common tools for 3D image processing
ngff
Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.