A perspective on FAIR quality control in multiplexed imaging data processing.
| Autor: | Vierdag WAM; Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany., Saka SK; Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. |
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| Jazyk: | angličtina |
| Zdroj: | Frontiers in bioinformatics [Front Bioinform] 2024 Feb 09; Vol. 4, pp. 1336257. Date of Electronic Publication: 2024 Feb 09 (Print Publication: 2024). |
| DOI: | 10.3389/fbinf.2024.1336257 |
| Abstrakt: | Multiplexed imaging approaches are getting increasingly adopted for imaging of large tissue areas, yielding big imaging datasets both in terms of the number of samples and the size of image data per sample. The processing and analysis of these datasets is complex owing to frequent technical artifacts and heterogeneous profiles from a high number of stained targets To streamline the analysis of multiplexed images, automated pipelines making use of state-of-the-art algorithms have been developed. In these pipelines, the output quality of one processing step is typically dependent on the output of the previous step and errors from each step, even when they appear minor, can propagate and confound the results. Thus, rigorous quality control (QC) at each of these different steps of the image processing pipeline is of paramount importance both for the proper analysis and interpretation of the analysis results and for ensuring the reusability of the data. Ideally, QC should become an integral and easily retrievable part of the imaging datasets and the analysis process. Yet, limitations of the currently available frameworks make integration of interactive QC difficult for large multiplexed imaging data. Given the increasing size and complexity of multiplexed imaging datasets, we present the different challenges for integrating QC in image analysis pipelines as well as suggest possible solutions that build on top of recent advances in bioimage analysis. Competing Interests: SKS is an inventor on patent applications related to multiplexed imaging and is a consulting scientific co-founder and shareholder for Digital Biology, Inc. The remaining author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2024 Vierdag and Saka.) |
| Databáze: | MEDLINE |
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