SAT: Segment and Track Anything for Microscopy

Nabeel Khalid, Nabeel Khalid, Mohammadmahdi Koochali, Khola Naseem, Khola Naseem, Maria Caroprese, Gillian Lovell, Daniel A. Porto, Johan Trygg, Johan Trygg, Andreas Dengel, Andreas Dengel, Sheraz Ahmed

2025

Abstract

Integrating cell segmentation with tracking is critical for achieving a detailed and dynamic understanding of cellular behavior. This integration facilitates the study and quantification of cell morphology, movement, and interactions, offering valuable insights into a wide range of biological processes and diseases. However, traditional methods rely on labor-intensive and costly annotations, such as full segmentation masks or bounding boxes for each cell. To address this limitation, we present SAT: Segment and Track Anything for Microscopy, a novel pipeline that leverages point annotations in the first frame to automate cell segmentation and tracking across all subsequent frames. By significantly reducing annotation time and effort, SAT enables efficient and scalable analysis, making it well-suited for large-scale studies. The pipeline was evaluated on two diverse datasets, achieving over 80% Multiple Object Tracking Accuracy (MOTA), demonstrating its robustness and effectiveness across various imaging modalities and cell types. These results highlight SAT’s potential to streamline biomedical research and enable deeper exploration of cellular behavior.

Paper Citation

in Harvard Style

Khalid N., Koochali M., Naseem K., Caroprese M., Lovell G., Porto D., Trygg J., Dengel A. and Ahmed S. (2025). SAT: Segment and Track Anything for Microscopy. In Proceedings of the 17th International Conference on Agents and Artificial Intelligence - Volume 2: ICAART; ISBN 978-989-758-737-5, SciTePress, pages 286-297. DOI: 10.5220/0013154200003890

in Bibtex Style

@conference{icaart25,
author={Nabeel Khalid and Mohammadmahdi Koochali and Khola Naseem and Maria Caroprese and Gillian Lovell and Daniel Porto and Johan Trygg and Andreas Dengel and Sheraz Ahmed},
title={SAT: Segment and Track Anything for Microscopy},
booktitle={Proceedings of the 17th International Conference on Agents and Artificial Intelligence - Volume 2: ICAART},
year={2025},
pages={286-297},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0013154200003890},
isbn={978-989-758-737-5},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 17th International Conference on Agents and Artificial Intelligence - Volume 2: ICAART
TI - SAT: Segment and Track Anything for Microscopy
SN - 978-989-758-737-5
AU - Khalid N.
AU - Koochali M.
AU - Naseem K.
AU - Caroprese M.
AU - Lovell G.
AU - Porto D.
AU - Trygg J.
AU - Dengel A.
AU - Ahmed S.
PY - 2025
SP - 286
EP - 297
DO - 10.5220/0013154200003890
PB - SciTePress