The ciliary ultrastructure can be damaged in various situations. Such changes include primary defects found in primary ciliary dyskinesia (PCD) and secondary defects developing in secondary ciliary dyskinesia (SCD). PCD is a genetic disease resulting from impaired ciliary motility causing chronic disease of the respiratory tract. SCD is an acquired condition that can be caused, for example, by respiratory infection or exposure to tobacco smoke. The diagnosis of these diseases is a complex process with many diagnostic methods, including the evaluation of ciliary ultrastructure using transmission electron microscopy (the golden standard of examination). Our goal was to create a program capable of automatic quantitative analysis of the ciliary ultrastructure, determining the ratio of primary and secondary defects, as well as analysis of the mutual orientation of cilia in the ciliary border. PCD Quant, a program developed for the automatic quantitative analysis of cilia, cannot yet be used as a stand-alone method for evaluation and provides limited assistance in classifying primary and secondary defect classes and evaluating central pair angle deviations. Nevertheless, we see great potential for the future in automatic analysis of the ciliary ultrastructure.

Clinical and Transplant Pathology Centre Institute for Clinical and Experimental Medicine Vídeňská 1958 140 21 Prague 4 Czech Republic

Department of Histology and Embryology 2nd Faculty of Medicine Charles University 5 Úvalu 84 150 06 Prague 5 Czech Republic

Department of Paediatrics 2nd Faculty of Medicine Charles University and Motol University Hospital 5 Úvalu 84 150 06 Prague 5 Czech Republic

Department of Pathology and Molecular Medicine 2nd Faculty of Medicine Charles University and Motol University Hospital 5 Úvalu 84 150 06 Prague 5 Czech Republic

Institute of Computer Engineering and Applied Informatics Faculty of Informatics and Information Technologies Slovak University of Technology Ilkovicova 2 84216 Bratislava Slovakia

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