Karyotyper

A karyotyper is a software tool or set of methods used in cytogenetics to automatically identify, classify, and organize chromosomes in images of metaphase spreads in order to produce a digital karyotype (karyogram). It supports researchers and clinicians by streamlining chromosome analysis and reducing manual labor.

In typical workflows, a user provides high-resolution chromosome images (often GTG- or other banding methods). The software segments each chromosome, traces its outline, detects the centromere, and assigns a chromosome class (for example, 1–22, X, Y) based on size, morphology, and banding patterns. Advanced implementations can group homologous chromosomes into pairs and arrange them according to standard conventions. Many systems offer semi-automatic operation, where the algorithm proposes calls that a human expert can confirm or adjust. Output includes a digital karyotype file and an ISCN-style report, annotating numerical abnormalities such as aneuploidy and structural changes like translocations, deletions, duplications, and inversions.

Methods commonly involve image processing, computer vision, and, increasingly, machine learning or deep learning for chromosome classification and band recognition. Applications span clinical cytogenetics laboratories—prenatal screening and cancer cytogenetics—and research settings. Tools may be open-source or commercial, and they may export data in standard formats compatible with ISCN nomenclature.

Limitations include dependence on image quality, overlapping or poorly resolved chromosomes, and mosaicism, which can complicate automated calls. Regardless, karyotypers are typically used in conjunction with expert review to ensure accurate interpretation.