The Cilialyzer – a freely available open-source software for a standardised identification of impaired mucociliary activity facilitating the diagnostic testing for PCD

Abstract

Background and Objective: Primary ciliary dyskinesia (PCD) is a rare genetic disorder causing a defective ciliary structure, which predominantly leads to an impaired mucociliary clearance and associated airway disease. As there is currently no single diagnostic gold standard test, PCD is diagnosed by a combination of several methods comprising genetic testing and the examination of the ciliary structure and function. Among the approved diagnostic methods, only high-speed video microscopy (HSVM) allows to directly observe the ciliary motion and therefore, to directly assess ciliary function. In the present work, we present our recently developed freely available open-source software - termed 'Cilialyzer, which has been specifically designed to support and facilitate the analysis of the mucociliary activity in respiratory epithelial cells captured by high- speed video microscopy. Methods: In its current state, the Cilialyzer software enables clinical PCD diagnosticians to load, preprocess and replay the image sequences with a feature-rich replaying module facilitating the commonly performed qualitative visual assessment of ciliary function. The image processing methods made accessible through an intuitive user interface allow clinical specialists to comfortably compute the ciliary beating frequency (CBF), the activity map and the 'frequency correlation length' - an observable getting newly introduced. Furthermore, the Cilialyzer contains a simple-to-use particle tracking interface to determine the mucociliary transport speed. Results: The Cilialyzer is fully written in the Python programming language and freely available under the terms of the MIT license. The proper functioning of the computational analysis methods constituting the Cilialyzer software is demonstrated by using simulated and representative sample data from clinical practice. Conclusions: The Cilialyzer serves as a useful clinical tool for standardised PCD diagnostics and provides new quantitative information awaiting to be clinically evaluated using cohorts of PCD. As the Cilialyzer is freely available under the terms of a permissive open-source license, it serves as a ground frame for further development of computational methods aiming at the quantification and automation of the analysis of mucociliary activity captured by HSVM.

Evaluation of Open-Source Ciliary Analysis Software in Primary Ciliary Dyskinesia: A Comparative Assessment

“…Image stabilization and motion extraction features may have improved signal quantification; Schneiter, et al demonstrated the importance of image stabilization in a freshly excised group of nasal epithelial cells exhibiting a superposed quasi-periodic motion on the ciliary function within the ROI [20]. This resulted in an inaccurate reading of the average power spectral density, which compromised both the display of the CBF-bandwidth, and the actual CBF peak value.…”

“…Before analyzing the frequency, the ROI was manually selected using the cropping function. For Cilialyzer, the RAW format video files were converted into sequence images in portable network graphics (PNG) format and pre-processed as stated by the Cilialyzer manual [20]. The preprocessing methods included initial manual image rotation, selecting ROI, image stabilization, cropping margins, and motion extraction.…”

“…The first commercially available software, Sisson-Ammons Video Analysis (SAVA) system, was developed in 2003 [18]. The development of freely available open-source software followed, which notably included the software named CiliaFA in 2012, but more recently, CiliarMove in 2021, and Cilialyzer in 2022 [17], [20], [21]. All the software applications mentioned above have individually demonstrated the capability to accurately calculate CBF, aligning with manually determined values [17], [18], [20], [21].…”

“…The development of freely available open-source software followed, which notably included the software named CiliaFA in 2012, but more recently, CiliarMove in 2021, and Cilialyzer in 2022 [17], [20], [21]. All the software applications mentioned above have individually demonstrated the capability to accurately calculate CBF, aligning with manually determined values [17], [18], [20], [21]. Among the available open-source software platforms, CiliarMove and Cilialyzer, have been validated independently in recent literature for their ability to perform such analyses [20], [21].…”

“…All the software applications mentioned above have individually demonstrated the capability to accurately calculate CBF, aligning with manually determined values [17], [18], [20], [21]. Among the available open-source software platforms, CiliarMove and Cilialyzer, have been validated independently in recent literature for their ability to perform such analyses [20], [21].…”