Aycromo: An Open-Source Platform for Automatic Chromosome Detection in Metaphase Images Based on Deep Learning

We present KAYRA, an end-to-end karyotyping system that operates inside the operational constraints of a clinical cytogenetic laboratory. KAYRA is architected as a containerized microservice pipeline whose ML stack combines an EfficientNet-B5 + U-Net semantic segmenter, a Mask R-CNN (ResNet-50 + FPN) instance detector, and a ResNet-18 classifier, orchestrated through a cascaded ROI-narrowing strategy that focuses each downstream model on the chromosome-bearing region. The same container images are deployed both as a cloud service and as an on-premise installation, supporting clinical environments where patient-data egress is not permitted as well as those where it is. A pilot clinical evaluation against two commercial reference karyotyping systems on 459 chromosomes from 10 metaphase spreads shows segmentation accuracy of 98.91 % (vs. 78.21 % / 40.52 %), classification accuracy of 89.1 % (vs. 86.9 % / 54.5 %), and rotation accuracy of 89.76 % (vs. 94.55 % / 78.43 %). KAYRA improves over the older density-thresholding reference on all three axes (p < 0.0001 for segmentation and classification by Fisher's exact test on chromosome-level counts), and on segmentation also against the modern AI- supported reference (p < 0.0001); on classification the difference vs. the modern AI reference is not statistically significant at the present test-set size (p = 0.34). The system reaches TRL 6 maturity and integrates the human-in-the-loop expert-review workflow that diagnostic cytogenetic practice requires. The thesis of this paper is that a multi-model cytogenetic AI service can be packaged as a microservice architecture supporting flexible deployment - cloud-hosted or on-premise - while delivering strong empirical performance on a pilot clinical evaluation.

Pathology foundation models (FMs) are models trained on vast amounts of typically unlabeled data and have been shown to yield regularized latent spaces that can be used effectively in downstream classification tasks. This is also true for the classification of mitotic figures vs. other cells. However, it is so far unclear if the latent space of current FMs provides features that are discriminant and spatially suitably resolved to also serve as a backbone for dense object detection paradigms. In this work, we investigate this question for common current pathology FMs (UNI, UNI2-h, Virchow, Virchow2, H-optimus-0, H-optimus-1) and compare their performance against a fully end-to-end trained baseline based on a ResNet50 architecture. We combine FM backbones with representatives of single stage, dual stage and self-attention-based detectors (RetinaNet, Faster R-CNN, Deformable DETR respectively) on the multi-domain MIDOG++ dataset, and on the TUPAC16 dataset as an out-of-domain case. We show that the H-optimus-0 and Virchow models yielded competitive performance, indicating that the latent spaces of current FMs, all trained on image-level self-supervision, are suitable for direct mitotic figure detection and may be slightly more robust on our out-of-domain test case. All code is made available publicly at https://github.com/DeepMicroscopy/FM4MFdet.

Neuron counting and segmentation in microscopy images of neuronal cultures is a routine and time-consuming task in neuroscience research, traditionally performed through manual inspection or semi-automatic tools. We present NeuroAdaptTrainer, an open-source Fiji/ImageJ plugin that integrates a YOLO instance-segmentation model directly into the microscopist's workflow. The plugin allows a user to run automatic neuron detection on a single image or a batch of images, manually correct the resulting detections from within Fiji, and use those corrections to adapt the model to new imaging conditions via transfer learning. A built-in external validation module allows the base and adapted models to be compared quantitatively on a held-out annotated set. NeuroAdaptTrainer lowers the barrier for non-specialist users to benefit from deep-learning-based segmentation while keeping expert supervision at the center of the workflow.