Simple analysis of gel images with IOCBIO Gel
Jaak Kütt, Georg Margus, Lauri Kask, Triinu Rätsepso, Kärol Soodla, Romain Bernasconi, Rikke Birkedal, Priit Järv, Martin Laasmaa, Marko Vendelin
BMC Biol, 2023 Oct 20; 21(1): 225.
- PMID: 37864184
- DOI: 10.1186/s12915-023-01734-8
Significance
Gel images underpin many common biochemical measurements, but their analysis is often difficult to reproduce because intermediate choices are not recorded. This published paper introduces IOCBIO Gel, a free, open-source program that links analysis results to the associated experimental metadata. It records the original image and each operation, including cropping, background subtraction, lane selection, and integration boundaries, so researchers can review and correct an analysis at any stage. By making gel-image workflows traceable and shareable, IOCBIO Gel supports more reliable results and FAIR data practices across Western blots and other gel-based techniques.
Abstract
BACKGROUND: Current solutions for the analysis of Western Blot images lack either transparency and reproducibility or can be tedious to use if one has to ensure the reproducibility of the analysis.
RESULTS: Here, we present an open-source gel image analysis program, IOCBIO Gel. It is designed to simplify image analysis and link the analysis results with the metadata describing the measurements. The software runs on all major desktop operating systems. It allows one to use it in either a single-researcher environment with local storage of the data or in a multiple-researcher environment using a central database to facilitate data sharing within the research team and beyond. By recording the original image and all operations performed on it, such as image cropping, subtraction of background, sample lane selection, and integration boundaries, the software ensures the reproducibility of the analysis and simplifies making corrections at any stage of the research. The analysis results are available either through direct access to the database used to store it or through the export of the relevant data.
CONCLUSIONS: The software is not only limited to Western Blot image analysis and can be used to analyze images obtained as a part of many other widely used biochemical techniques such as isoelectric focusing. By recording the original data and all the analysis steps, the program improves reproducibility in the analysis and contributes to the implementation of FAIR principles in the related fields.
Keywords: Data analysis; FAIR; Isoelectric focusing; Reproducibility; Southern blotting; Western blotting.