6 papers
Fast Cubical Persistent Homology on 2D and 3D Images via Union-Find, Pruning, and Lookup Tables
Titouan Le Breton, Karol Szustakowski, Marie Piraud
We present Flash Cubical, a highly efficient computation of cubical persistence on a V-filtration for 2D and 3D images over . The implementation is built around three…
Leveraging Multi-Rater Annotations to Calibrate Object Detectors in Microscopy Imaging
Francesco Campi, Lucrezia Tondo, Ekin Karabati +2
Deep learning-based object detectors have achieved impressive performance in microscopy imaging, yet their confidence estimates often lack calibration, limiting their reliability f…
Preserving instance continuity and length in segmentation through connectivity-aware loss computation
Karol Szustakowski, Luk Frank, Julia Esser +2
In many biomedical segmentation tasks, the preservation of elongated structure continuity and length is more important than voxel-wise accuracy. We propose two novel loss functions…
Forest-Guided Clustering -- Shedding Light into the Random Forest Black Box
Lisa Barros de Andrade e Sousa, Gregor Miller, Ronan Le Gleut +3
As machine learning models are increasingly deployed in sensitive application areas, the demand for interpretable and trustworthy decision-making has increased. Random Forests (RF)…
OneProt: Towards Multi-Modal Protein Foundation Models
Klemens Flöge, Srisruthi Udayakumar, Johanna Sommer +8
Recent advances in Artificial Intelligence have enabled multi-modal systems to model and translate diverse information spaces. Extending beyond text and vision, we introduce OnePro…
MultiOrg: A Multi-rater Organoid-detection Dataset
Christina Bukas, Harshavardhan Subramanian, Fenja See +8
High-throughput image analysis in the biomedical domain has gained significant attention in recent years, driving advancements in drug discovery, disease prediction, and personaliz…