Related Experiment Video
Updated: Jun 16, 2026
Using Computer Vision Libraries to Streamline Nuclei Quantification
Published on: June 6, 2025
QATS: an ImageJ plugin for the quantification of toroidal nuclei in biological images
Carles Pons1, Caroline Mauvezin2,3
1Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology (BIST), 08028 Barcelona, Spain.
Motivation:
The toroidal nucleus is a novel chromosomal instability (CIN) biomarker which complements the micronucleus. Understanding the specific biological stresses leading to the formation of each CIN-associated phenotype requires the evaluation of large panels of biological images collected from different genetic backgrounds and environmental conditions. However, the quantification of toroidal nuclei is currently a manual process which is unviable on a large scale.
Results:
Here, we present QATS (QuAntification of Toroidal nuclei in biological imageS), a tool that automates the identification of toroidal nuclei, minimizing false positives while highly agreeing with the manual quantifications. Additionally, QATS identifies micronuclei for a convenient comparison of both CIN biomarkers. QATS is an open-source ImageJ plugin with a user-friendly interface that enables a wide scientific community to easily assess the frequency of CIN biomarkers for the determination of CIN levels in cellular models.
Availability And Implementation:
QATS is an ImageJ plugin freely available at http://www.toroidalnucleus.org/qats. The user manual and the images used for the evaluation of QATS are included in the website. Supplementary data are available at Bioinformatics online.
