euro-bioimaging Goto Github PK

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.

data

Example data that can be used to test tools.

galaxy-image-analysis

Galaxy tools for image analysis

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

ngff

Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.

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