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 ...

This KNIME workflow is designed to facilitate the loading of image data from OMERO. It includes key preprocessing steps for VAST data, such as metadata creation and the linking of Key-Value Pairs.

• Fetching Images: The first step involves fetching images from a locally accessible folder.
• User Authentication: Users are prompted to input their OMERO username and password through a Java snippet. This information is then converted into variables that can be used by the Python script node. ...

Workflow to perform nuclei cell counting on High Content Screening (HCS) Data and upload result into OMERO

In this workflow, cell images are first uploaded to both Galaxy and OMERO using the “OMERO Image Import” tool. Concurrently, image processing is performed. After thresholding and binarization, key features of nuclei, such as area, label number, and perimeter, are computed from the processed images and saved as a CSV file. The result file is then attached to each image stored in OMERO using ...

General workflow to upload data into OMERO using Galaxy

A dataset for testing can be found at: https://zenodo.org/records/14205500

Important Security Note: It is crucial to be aware that storing credentials as variables can pose security risks, particularly if accessed by administrators. Therefore, it is essential to handle user credentials securely and in accordance with best practices.

General workflow to upload data into OMERO using KNIME

The workflow consists of two main branches: the Green Branch, which imports a folder containing images, and the Purple Branch, which enables the annotation of metadata as key-value pairs.

• Fetching Images: The first step involves fetching images from a locally accessible folder.
• User Authentication: Users are prompted to input their OMERO username and password through a Java snippet. This information is then converted into ...