Membrane Thickness Distribution Analysis of Mouse Kidney Glomeruli

The MATLAB script in this repository is designed to accompany our manuscript submission to Kidney International by Ali et al in 2024. The `ThicknessDistribution.m` function analyzes 3D fluorescent image data to quantify the thickness distribution of biological specimens. By processing both raw image stacks and their corresponding binary masks, this function generates accurate measurements of specimen thickness, which is critical in various biological applications. The main scripts along with example raw and mask images, and some useful function scripts are included:

Matlab Files:

ThicknessDistribution.m 

readBigTiff.m

To help load larger imageJ saved tif datasets

find_pulse.m

To help restrict only the largest major peak from the intensity profiles

readme.doc

Example image files:

Test_Raw.tif

A cropped ROI region of a mouse kidney glomerular Bowman's capsule basement membrane

Test_Mask.tif

The segmented mask that corresponds to the Test_Raw.tif.

Output images from the script:

Test_mesh.PNG

Test_histogram.PNG

Test_IntensityGausFit.PNG

Test_ThicknessMap.PNG