This repository contains scripts to quantify ciliary proteins in cilia from Leica image files. These scripts were developed by Bhaven Patel and Maia Kinnebrew, with help from Dr. Onn Brandman, in the Rohatgi Lab in the Department of Biochemsitry in the Stanford School of Medicine. Please contact Bhaven Patel at [email protected] with any questions.

The “cilia_SMO_quantification” folder contains the scripts to quantify proteins, such as Smoothened and Patched1, which are not always localized to one specific area of the cilia. Therefore, the quantification from these scripts is a bulk measurement of the protein-of-interest (POI) in the cilia. Please note that since this script was developed using test images in which acetylated-tubulin was used as a cilia marker, a special criteria was added to reduce false-positives when identifying cilia. When creating a mask of the acetylated-tubulin channel, small cilia-like objects are sometimes formed from non-specific staining, so we created a check that throws out any cilia object that has another object within a defined distance. This helps filter out false-positives, but does create some false-negatives. A more detailed “README.txt” file within this folder contains the specifics of the scripts and how to use the scripts in MATLAB.

The “cilia_Gli2_quantification” folder contains the scripts to quantify proteins, such as Gli2 or Iqce, which are often localized to a specific area of the cilia. The quantification from these scripts is a defined measurement of the protein-of-interest (POI) in the cilia. Please note that since this script was developed using test images in which acetylated-tubulin was used as a cilia marker, a special criteria was added to reduce false-positives when identifying cilia. When creating a mask of the acetylated-tubulin channel, small cilia-like objects are sometimes formed from non-specific staining, so we created a check that throws out any cilia object that has another object within a defined distance. This helps filter out false-positives, but does create some false-negatives. A more detailed “README.txt” file within this folder contains the specifics of the scripts and how to use the scripts in MATLAB.