detectCilia: An R Package for Automated Detection and Length Measurement of Primary Cilia

Area of Science:

• Cell Biology
• Microscopy Imaging Analysis

Background:

• Primary cilia are vital cellular antennae involved in cell signaling.
• Cilia length is critical for function, necessitating reproducible measurement methods.
• Automated tools are needed to study cilia length changes due to physical or chemical stimuli.

Purpose of the Study:

• To introduce detectCilia, an open-source R package for automatic primary cilia detection and measurement.
• To demonstrate detectCilia's capability by comparing primary cilia lengths in human chondrocytes cultured in various media.
• To evaluate detectCilia's performance against existing tools like ACDC and CiliaQ.

Main Methods:

• Developed and validated the 'detectCilia' R package for automated image analysis.
• Applied detectCilia to measure primary cilia length in human chondrocytes.
• Compared four different cell culture media: ITS, ITS+Dexa, ITS+Dexa+IGF-1+TGF-β1, and FBS.
• Benchmarked detectCilia against ACDC and CiliaQ.

Main Results:

• detectCilia provides accurate and reproducible primary cilia length measurements.
• Significant variations in primary cilia length were observed across the tested cell culture media.
• detectCilia demonstrated advantages over ACDC and CiliaQ in performance and usability.

Conclusions:

• detectCilia is a valuable tool for automated, reproducible primary cilia detection and measurement from confocal microscopy images.
• The package offers low false-positive rates and minimal user intervention.
• The study highlights the impact of different media compositions on primary cilia length in chondrocytes.