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BASIN: A Semi-automatic Workflow, with Machine Learning Segmentation, for Objective Statistical Analysis of

Timothy W Hartman1, Evgeni Radichev1, Hafiz Munsub Ali1

  • 1Biomedical Engineering Department, University of South Dakota Sioux Falls, 4800 N Career Avenue, Sioux Falls, SD 57107, United States.

Journal of Molecular Biology
|December 4, 2022
PubMed
Summary

Bioimage Analysis, Statistic, and Comparison (BASIN) software offers objective micrograph comparisons using inferential statistics. This tool enhances bioscience research reproducibility and data integration, achieving 78% accuracy in initial assessments.

Keywords:
FAIRMicrobebiofilmcancerimage comparisonmachine learningmicroscope imagingsegmentationstatistical analysis

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Area of Science:

  • Biosciences
  • Bioimage Analysis
  • Scientific Research

Background:

  • Micrograph comparison is crucial in biosciences for assessing experimental conditions.
  • Current methods often rely on subjective visual interpretation for two-condition comparisons.
  • Bridging image data with other modalities requires objective and reproducible analysis.

Purpose of the Study:

  • To develop and validate the Bioimage Analysis, Statistic, and Comparison (BASIN) software.
  • To provide an objective and reproducible method for micrograph comparison in biosciences.
  • To enhance accessibility through R Shiny implementation (online and offline versions).

Main Methods:

  • Implemented machine learning-based object segmentation within BASIN.
  • Integrated inferential statistics for quantitative data extraction (object counts, intensities, areas).
  • Developed BASIN using R Shiny for improved accessibility and user experience.

Main Results:

  • Processed 498 image pairs across five bioscience topics.
  • BASIN achieved 78% accuracy in manual curation-based assessments.
  • Initial BASIN versions demonstrated an average 82% FAIR compliance score.

Conclusions:

  • BASIN software offers an objective and reproducible approach to micrograph comparison.
  • The tool effectively bridges image data with other experimental modalities.
  • BASIN enhances data analysis capabilities and research reproducibility in biosciences.