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Image-based cell profiling enhancement via data cleaning methods

Rezvani, A ; Sharif University of Technology | 2022

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  1. Type of Document: Article
  2. DOI: 10.1371/journal.pone.0267280
  3. Publisher: Public Library of Science , 2022
  4. Abstract:
  5. With the advent of high-throughput assays, a large number of biological experiments can be carried out. Image-based assays are among the most accessible and inexpensive technologies for this purpose. Indeed, these assays have proved to be effective in characterizing unknown functions of genes and small molecules. Image analysis pipelines have a pivotal role in translating raw images that are captured in such assays into useful and compact representation, also known as measurements. CellProfiler is a popular and commonly used tool for this purpose through providing readily available modules for the cell/nuclei segmentation, and making various measurements, or features, for each cell/nuclei. Single cell features are then aggregated for each treatment replica to form treatment “profiles”. However, there may be several sources of error in the CellProfiler quantification pipeline that affects the downstream analysis that is performed on the profiles. In this work, we examined various preprocessing approaches to improve the profiles. We consider the identification of drug mechanisms of action as the downstream task to evaluate such preprocessing approaches. Our enhancement steps mainly consist of data cleaning, cell level outlier detection, toxic drug detection, and regressing out the cell area from all other features, as many of them are widely affected by the cell area. Our experiments indicate that by performing these time-efficient preprocessing steps, image-based profiles can preserve more meaningful information compared to raw profiles. In the end, we also suggest possible avenues for future research. © 2022 Rezvani et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
  6. Keywords:
  7. Algorithm ; Cell activity ; Cell death ; Cell profiling ; Cell viability ; Cleaning ; Deep learning ; Drug development ; Drug mechanism ; Drug toxicity ; Error ; High throughput analysis ; Histogram ; Human ; Hypothesis ; Image analysis ; Linear regression analysis ; Machine learning ; Mathematical model ; Microscopy ; Outlier detection ; Phenotype ; Pipeline ; Toxicity ; Training ; Cell nucleus ; Image enhancement ; Image processing ; Procedures ; Image Processing, Computer-Assisted
  8. Source: PLoS ONE ; Volume 17, Issue 5 May , 2022 ; 19326203 (ISSN)
  9. URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0267280