Segmentation of fish chromosomes in microscopy images: A new dataset

  • Rodrigo Rodrigues UFV
  • Rubens Pasa UFV
  • Karine Kavalco UFV
  • João Fernando Mari UFV


The chromosome segmentation is the most important step in automatic karyotype assembling. In this work, we presented a brand new chromosome image dataset and proposed methods for segmenting the chromosomes. Chromosome images are usually low quality, especially fish chromosomes. In order to overcome this issue, we tested three filters to reduce noise and improve image quality. After filtering, we applied adaptive threshold segmentation combined with mathematical morphology and supervised classification methods. Support Vector Machine and k-nearest neighbors were applied to discriminate between chromosomes and image background. The proposed method was applied to segment chromosomes in a new dataset. To enable measure the performance of the methods all chromosomes were manually delineated. The results are evaluated considering the Hausdorff distance and normalized sum of distances between segmented and reference images.

Palavras-chave: Fish karyotype, chromosome segmentation, computer vision, classification, new dataset


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RODRIGUES, Rodrigo; PASA, Rubens; KAVALCO, Karine; MARI, João Fernando. Segmentation of fish chromosomes in microscopy images: A new dataset. In: WORKSHOP DE VISÃO COMPUTACIONAL (WVC), 16. , 2020, Evento Online. Anais [...]. Porto Alegre: Sociedade Brasileira de Computação, 2020 . p. 58-63. DOI: