Simple analysis of gel images with IOCBIO Gel
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...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2023-10-01
|
| Series: | BMC Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12915-023-01734-8 |
| _version_ | 1797556442315620352 |
|---|---|
| author | Jaak Kütt Georg Margus Lauri Kask Triinu Rätsepso Kärol Soodla Romain Bernasconi Rikke Birkedal Priit Järv Martin Laasmaa Marko Vendelin |
| author_facet | Jaak Kütt Georg Margus Lauri Kask Triinu Rätsepso Kärol Soodla Romain Bernasconi Rikke Birkedal Priit Järv Martin Laasmaa Marko Vendelin |
| author_sort | Jaak Kütt |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T17:01:57Z |
| format | Article |
| id | doaj.art-7a20e639c19f404a9cffde58d3839d34 |
| institution | Directory Open Access Journal |
| issn | 1741-7007 |
| language | English |
| last_indexed | 2024-03-10T17:01:57Z |
| publishDate | 2023-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Biology |
| spelling | doaj.art-7a20e639c19f404a9cffde58d3839d342023-11-20T10:55:37ZengBMCBMC Biology1741-70072023-10-0121111010.1186/s12915-023-01734-8Simple analysis of gel images with IOCBIO GelJaak Kütt0Georg Margus1Lauri Kask2Triinu Rätsepso3Kärol Soodla4Romain Bernasconi5Rikke Birkedal6Priit Järv7Martin Laasmaa8Marko Vendelin9Laboratory of Systems Biology, Department of Cybernetics, Tallinn University of TechnologyLaboratory of Systems Biology, Department of Cybernetics, Tallinn University of TechnologyLaboratory of Systems Biology, Department of Cybernetics, Tallinn University of TechnologyLaboratory of Systems Biology, Department of Cybernetics, Tallinn University of TechnologyLaboratory of Systems Biology, Department of Cybernetics, Tallinn University of TechnologyLaboratory of Systems Biology, Department of Cybernetics, Tallinn University of TechnologyLaboratory of Systems Biology, Department of Cybernetics, Tallinn University of TechnologyApplied Artificial Intelligence Group, Department of Software Science, Tallinn University of TechnologyLaboratory of Systems Biology, Department of Cybernetics, Tallinn University of TechnologyLaboratory of Systems Biology, Department of Cybernetics, Tallinn University of TechnologyAbstract 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.https://doi.org/10.1186/s12915-023-01734-8Data analysisReproducibilityFAIRWestern blottingSouthern blottingIsoelectric focusing |
| spellingShingle | Jaak Kütt Georg Margus Lauri Kask Triinu Rätsepso Kärol Soodla Romain Bernasconi Rikke Birkedal Priit Järv Martin Laasmaa Marko Vendelin Simple analysis of gel images with IOCBIO Gel BMC Biology Data analysis Reproducibility FAIR Western blotting Southern blotting Isoelectric focusing |
| title | Simple analysis of gel images with IOCBIO Gel |
| title_full | Simple analysis of gel images with IOCBIO Gel |
| title_fullStr | Simple analysis of gel images with IOCBIO Gel |
| title_full_unstemmed | Simple analysis of gel images with IOCBIO Gel |
| title_short | Simple analysis of gel images with IOCBIO Gel |
| title_sort | simple analysis of gel images with iocbio gel |
| topic | Data analysis Reproducibility FAIR Western blotting Southern blotting Isoelectric focusing |
| url | https://doi.org/10.1186/s12915-023-01734-8 |
| work_keys_str_mv | AT jaakkutt simpleanalysisofgelimageswithiocbiogel AT georgmargus simpleanalysisofgelimageswithiocbiogel AT laurikask simpleanalysisofgelimageswithiocbiogel AT triinuratsepso simpleanalysisofgelimageswithiocbiogel AT karolsoodla simpleanalysisofgelimageswithiocbiogel AT romainbernasconi simpleanalysisofgelimageswithiocbiogel AT rikkebirkedal simpleanalysisofgelimageswithiocbiogel AT priitjarv simpleanalysisofgelimageswithiocbiogel AT martinlaasmaa simpleanalysisofgelimageswithiocbiogel AT markovendelin simpleanalysisofgelimageswithiocbiogel |