e-learning
Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools
Abstract
Electrophoresis gel images are fundamental tools in molecular biology and biochemistry for separating DNA, RNA, or protein fragments by size or charge. Quantification of these bands allow for estimating product yield, comparing amplification efficiency, verifying PCR products, calculating molecular weights, and assessing enzyme activity or protein purity.
About This Material
This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.
Questions this will address
- How can specific bands on an electrophoresis gel image be selected using QuPath?
- How is a region of interest (ROI) GeoJSON file prepared?
- How are bands labeled and quantified using Galaxy tools?
- What outputs are generated during the analysis?
Learning Objectives
- Learn how to select bands on an electrophoresis gel image
- Generate ROI files in QuPath and process them in Galaxy
- Quantify band intensity and extract tabular results
Licence: Creative Commons Attribution 4.0 International
Keywords: DNA, Imaging, Protein, RNA, bioimaging
Target audience: Students
Resource type: e-learning
Version: 1
Status: Active
Prerequisites:
- FAIR Bioimage Metadata
- Introduction to Galaxy Analyses
- Introduction to Image Analysis using Galaxy
- REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data
Learning objectives:
- Learn how to select bands on an electrophoresis gel image
- Generate ROI files in QuPath and process them in Galaxy
- Quantify band intensity and extract tabular results
Date modified: 2025-08-11
Date published: 2025-08-11
Contributors: Leonid Kostrykin
Scientific topics: Imaging
Activity log
