Automated Morphological Profiling via Deep Learning-Based Segmentation for High-Throughput Phenotypic Screening

H. Zováthi Bendegúz; Kainz Philipp: Automated Morphological Profiling via Deep Learning-Based Segmentation for High-Throughput Phenotypic Screening.
JOURNAL OF IMAGING, 12 (4). ISSN 2313-433X (2026)

Szöveg
jimaging-12-00179-v3.pdf - Megjelent verzió
Download (7MB)

Mű típusa:

Folyóiratcikk

Szerző azonosítók:

Név	ORCID	MTMT szerző azonosító
H. Zováthi Bendegúz	0000-0003-4298-635X	10103981
Kainz Philipp	0000-0001-7970-370X

Absztrakt (kivonat):

Reproducible morphological profiling, particularly for drug discovery, has become an important tool for compound evaluation. Established workflows such as CellProfiler provide a widely adopted foundation for Cell Painting analysis. However, conventional pipelines often require substantial manual configuration and technical expertise, which can limit scalability and accessibility. In this study, a fully automated deep learning-based workflow is presented for segmentation-driven morphological profiling from raw microscopy data. Using a curated subset of the JUMP Cell Painting pilot dataset, ground-truth masks were generated and used to train a U-net–based segmentation model in the IKOSA platform. Post-processing strategies were introduced to improve instance separation and reduce segmentation artifacts. The final model achieved strong segmentation performance (precision/recall/AP up to 0.98/0.94/0.92 for nuclei), with an average runtime of 2.2 s per 1080 × 1080 image. Segmentation outputs enabled large-scale feature extraction, yielding 3664 morphological descriptors that showed high correlation with CellProfiler-derived measurements (normalized MAE: 0.0298). Feature prioritization further reduced redundancy to 1145 informative descriptors. These results demonstrate that automated deep learning pipelines can complement established Cell Painting workflows by reducing configuration overhead while maintaining compatibility with validated morphological profiling standards. The proposed workflow may help improve resource efficiency in drug discovery and personalized medicine.

Folyóirat címe:

JOURNAL OF IMAGING

Megjelenés éve:

2026

Kötet:

Szám:

ISSN:

2313-433X

Intézmény:

Pázmány Péter Katolikus Egyetem

Kar:

Információs Technológiai és Bionikai Kar (2013.07.-)