Workflow Overview

This Galaxy workflow allows transferring ARC imaging data stored as .ZIP file to a target OMERO instance by 1) keeping the ARC structure and 2) automatize the metadata annotation of the assay.

How does it works

The workflow extract all the ./assays/experiment/dataset/ file path and create an OMERO dataset containing the images. The "isa.assay.xlsx" file is used to add key-value pairs to the dataset.

Workflow Inputs

The workflow as three different data inputs: ...

Basic workflow to upload images into OMERO together with ROIs

Associated Tutorial

This workflows is part of the tutorial Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy, available in the GTN

Features

• Includes a Galaxy Workflow Report ...

BioimageAIpub

A Python library to publish Bioimaging datasets to HuggingFace in AI-ready fashion.

Installation

git clone https://github.com/German-BioImaging/bioimageaipub/bioimageaipub.git 
cd bioimageaipub 
pip install -r requirements.txt 

Usage

BioimageAIpub is supplied as a Python library. See demo/demo.ipynb for a Python notebook demonstrating the usage.

Citation

Acknowledgments

This project was supported by and is attributable to the German Cancer Research Center (DKFZ) ...