Cilia Analysis

We have had a number of people analyze Cilia in the Core and ask us questions about how to analyze their cilia, primarily in terms of segmenting then measuring

NIS Elements

• A popular method inspired by this paper: https://pmc.ncbi.nlm.nih.gov/articles/PMC8791558/
• Easy to use and get set up on
• The basics is to Train with the Elements Ai (pixel-based machine learning), then analyze with a pipeline in the software
• Great for segmenting in 2D or 3D, then measuring fluorescence/size and shape
• NOTE: Steps acquiring on a microscope that uses micro-manager for easier import/NIS Elements
  • Capture stacks using the relative method instead of absolute
  • Save as tiff sequence (can also save as ome.tiff if preffered and run a macro to convert if you don’t mind the extra step)
  • Use the Converting tiff seq to ND2 PDF below to get your images in to NIS-elements

📄 Converting tiff seq to ND2

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CiliaQ

• CiliaQ: a simple, open-source software for automated quantification of ciliary morphology and fluorescence in 2D, 3D, and 4D images - PubMed
• Recommended by our specialist Micaela Lasser who used it in her paper! Ciliary biology intersects autism and congenital heart disease - PubMed