Javier Rico

Attila Pintér, Javier Rico, Attila Répai et al.

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.

Lukas Uzolas, Javier Rico, Pierrick Coupé et al.

Advances in deep-learning-based pipelines have led to breakthroughs in a variety of microscopy image diagnostics. However, a sufficiently big training data set is usually difficult to obtain due to high annotation costs. In the case of banded chromosome images, the creation of big enough libraries is difficult for multiple pathologies due to the rarity of certain genetic disorders. Generative Adversarial Networks (GANs) have proven to be effective in generating synthetic images and extending training data sets. In our work, we implement a conditional adversarial network that allows generation of realistic single chromosome images following user-defined banding patterns. To this end, an image-to-image translation approach based on self-generated 2D chromosome segmentation label maps is used. Our validation shows promising results when synthesizing chromosomes with seen as well as unseen banding patterns. We believe that this approach can be exploited for data augmentation of chromosome data sets with structural abnormalities. Therefore, the proposed method could help to tackle medical image analysis problems such as data simulation, segmentation, detection, or classification in the field of cytogenetics.