COMPASS: Comet Object Measurement Pipeline with Automated Selection and Scoring

Chromosome analysis is a fundamental step in the diagnosis of genetic diseases, but the manual karyotyping workflow is time-consuming and heavily dependent on expert specialists, often requiring several days per patient. Although Deep Learning models have achieved high performance in chromosome detection, most proposed solutions remain restricted to research prototypes or lack graphical interfaces suitable for clinical use. In this work, we present Aycromo, an open-source desktop platform for AI-assisted cytogenetic analysis. Built on Electron and ONNX Runtime, the tool allows cytogeneticists to load pre-trained models, compare architectures through an integrated benchmarking module, and manually correct detections via an interactive annotation interface, all without command-line interaction. Preliminary experiments on metaphase images from the CRCN-NE dataset demonstrate that YOLOv11 achieves 99.40% mAP@50, while the platform reduces per-slide analysis to seconds

Microscopy images contain rich information about how cells respond to perturbations, making them essential to applications like drug screening. To quantify images, researchers often use representation extraction methods, and recent years have seen a proliferation of deep learning methods. While measuring the quality of these representations is essential, evaluation remains fragmented, with each proposed model evaluated on different tasks and datasets, using custom pipelines and metrics, making it difficult to fairly compare models. Here, we introduce MorphoHELM, a comprehensive open benchmark for evaluating feature extraction methods for Cell Painting, the most widely-used morphological profiling assay. MorphoHELM consolidates evaluation standards in the field, extends and corrects them to be more robust, and evaluates on the widest range of methods to date. A defining feature of the benchmark is that each task is evaluated at different degrees of batch effects (or technical noise), directly quantifying how the ability of methods to detect biological signal degrades as noise increases. Together, these properties enable MorphoHELM to detect trade-offs between methods, and we demonstrate that models that excel at certain kinds of biological signal are weaker at others. We show that no existing model outperforms classic computer vision analytic strategies across all settings, which remain the strongest general use-case representations. All datasets, code, and evaluation tools are publicly available at https://github.com/microsoft/MorphoHELM.

Counting living cells is an important step in many biological research workflows. Our collaborators at the Wellcome Sanger Institute study vital genes in humans via large scale saturation genome editing screening, which requires repeatedly counting cells a great number of times. Computer Vision based automation is crucial for high throughput and resource efficiency. In this work, we develop a regression-based deep learning computer vision algorithm to detect and count cells in phase-contrast microscopy images. To reduce annotation effort, which in practice often becomes a bottleneck, we focus on counting cells only using sparse point annotations, which are fast and easy to acquire. By comparison to state-of-the-art 0-shot methods, we show that regression-based counting is a promising alternative in low data regimes. Through developing methods to automatically count living cells in microscopy images, we contribute to valuable research on the human genome. The code is available at https://github.com/beijn/cellnet.