Rassmann, S. | Search bioRxiv

bioRxiv2020

CiliaQ - a simple, open-source software for automated quantification of ciliary morphology and fluorescence in 2D, 3D, and 4D images

Cilia are hair-like membrane protrusions that emanate from the surface of most vertebrate cells and are classified into motile and primary cilia. Motile cilia move fluid flow or propel cells, while also fulfilling sensory functions. Primary cilia are immotile and act as a cellular antenna, translating environmental cues into cellular responses. Ciliary dysfunction leads to severe diseases, commonly termed ciliopathies. The molecular details underlying ciliopathies and ciliary function are, however, not well understood. Since cilia are small subcellular compartments, imaging-based approaches have been used to study them. However, tools to comprehensively analyze images are lacking. Automatic analysis approaches require commercial software and are limited to 2D analysis and only a few parameters. The widely used manual analysis approaches are time consuming, user-biased, and difficult to compare. Here, we present CiliaQ, a package of open-source, freely-available, and easy-to-use ImageJ plugins. CiliaQ allows high throughput analysis of 2D and 3D, static or time-lapse images from fluorescence microscopy of cilia in cell culture or tissues, and outputs a comprehensive list of parameters for ciliary morphology, length, bending, orientation, and fluorescence intensity, making it broadly applicable. We envision CiliaQ as a resource and platform for reproducible and comprehensive analysis of ciliary function in health and disease.

cell biology↗

bioRxiv2018

SpermQ - a simple analysis software to comprehensively study flagellar beating and sperm steering

Motile cilia, also called flagella, drive cell motility across a broad range of species; some cilia propel prokaryotes and eukaryotic cells like sperm, while cilia on epithelial surfaces create complex fluid patterns e.g. in the brain or lung. For sperm, the picture has emerged that the motile cilium, also called flagellum, is not only a motor, but also a sensor that detects stimuli from the environment, computing the beat pattern according to the sensory input. Thereby, the flagellum of the sperm cell navigates the sperm through a complex environment like the female genital tract. However, we know very little about how environmental signals change the flagellar beat and, thereby, the swimming behaviour of sperm. It has been proposed that distinct signalling domains in the flagellum control the flagellar beat. A detailed analysis has been mainly hampered by the fact that current comprehensive analysis approaches rely on complex microscopy and analysis systems. Thus, knowledge on sperm signalling regulating the flagellar beat is based on custom quantification approaches that are limited to only a few aspects of the flagellar beat, do not resolve the kinetics of the entire flagellum, rely on manual, qualitative descriptions, and are little comparable among each other. Here, we present SpermQ, a ready-to-use and comprehensive analysis software to quantify sperm motility. SpermQ provides a detailed quantification of the flagellar beat based on common time-lapse images acquired by dark-field or epi-fluorescence microscopy, making SpermQ widely applicable. We envision SpermQ becoming a standard tool in flagellar and motile cilia research that allows to readily link studies on individual signalling components in sperm and distinct flagellar beat patterns.

cell biology↗