Dataset Information

Automated, image-based quantification of peroxisome characteristics with perox-per-cell.

ABSTRACT:

Summary

perox-per-cell automates cumbersome, image-based data collection tasks often encountered in peroxisome research. The software processes microscopy images to quantify peroxisome features in yeast cells. It uses off-the-shelf image processing tools to automatically segment cells and peroxisomes and then outputs quantitative metrics including peroxisome counts per cell and spatial areas. In validation tests, we found that perox-per-cell output agrees well with manually quantified peroxisomal counts and cell instances, thereby enabling high-throughput quantification of peroxisomal characteristics.

Availability and implementation

The software is coded in Python. Compiled executables and source code are available at https://github.com/AitchisonLab/perox-per-cell.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Neal ML

PROVIDER: S-EPMC11269463 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Automated, image-based quantification of peroxisome characteristics with perox-per-cell.

Neal Maxwell L ML Shukla Nandini N Mast Fred D FD Farré Jean-Claude JC Pacio Therese M TM Raney-Plourde Katelyn E KE Prasad Sumedh S Subramani Suresh S Aitchison John D JD

Bioinformatics (Oxford, England) 20240713

<h4>Summary</h4>perox-per-cell automates cumbersome, image-based data collection tasks often encountered in peroxisome research. The software processes microscopy images to quantify peroxisome features in yeast cells. It uses off-the-shelf image processing tools to automatically segment cells and peroxisomes and then outputs quantitative metrics including peroxisome counts per cell and spatial areas. In validation tests, we found that perox-per-cell output agrees well with manually quantified pe ...[more]

PMID: 39001800

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Dataset Information

Automated, image-based quantification of peroxisome characteristics with perox-per-cell.

Summary

Availability and implementation

Supplementary information

Publications

Automated, image-based quantification of peroxisome characteristics with perox-per-cell.

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