An example how ISCC codes can be used to verify image analysis steps

Associated Tutorial

This workflows is part of the tutorial Content Tracking and Verification in Galaxy Workflows with ISCC-SUM, available in the GTN

Features

• Includes Galaxy Workflow Tests

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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) ...

Learning Objectives

• How to build complex queries using the IDR searcher to retrieve data from the Image Data Resource (IDR)
• How to load binary data from IDR using its Python API

Launch

This notebook can be launched using Google Colab.

The present workflow allows to perform 2D spots/blobs detection on specific channel and stack of an image. Images will be directly fetched from IDR by including the IDs. A pre-processing steps with histogram normalization is performed before the blobs detection.

Associated Tutorial

This workflows is part of the tutorial Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines, ...

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 ...

BatchConvert

A command line tool for converting image data into either of the standard file formats OME-TIFF or OME-Zarr.

The tool wraps the dedicated file converters bfconvert and bioformats2raw to convert into OME-TIFF or OME-Zarr, respectively. The workflow management system NextFlow is used to perform conversion in parallel for batches of images.

The tool also wraps s3 and Aspera clients (go-mc and aspera-cli, respectively). ...

Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures