![]() Here, we present CiliaQ, a package of open-source, freely available, and easy-to-use ImageJ plugins. The widely used manual analysis approaches are time consuming, user-biased, and difficult to compare. ![]() Automatic analysis approaches require commercial software and are limited to 2D analysis and only a few parameters. However, tools to comprehensively analyze images are lacking. ![]() Since cilia are small subcellular compartments, imaging-based approaches have been used to study them. The molecular details underlying ciliopathies and ciliary function are, however, not well understood. Ciliary dysfunction leads to severe diseases, commonly termed ciliopathies. Primary cilia are immotile and act as a cellular antenna, translating environmental cues into cellular responses. Motile cilia move fluid flow or propel cells, while also fulfill sensory functions. Cilia are hair-like membrane protrusions that emanate from the surface of most vertebrate cells and are classified into motile and primary cilia.
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