The ways that fibroblast cells remodel their local microenvironment is critical to a number of pathologies. To quantify this in a 3D environment, I an existing MATLAB script was modified to process the qualitative, visual information from confocal microscopy images and generate quantitative graphs representing the density of collagen around a fibroblast as a function of distance from the cell. While the earlier script used each 2D image from a confocal image stack and dilated the shape of the recognized cell to extract to find the coordinates of the surrounding collagen. The work in this study builds on the analysis of the collagen density around an active fibroblast. Instead of setting a threshold and identifying the cell in each 2D image, the new method uses all the stack images collected and builds a 3D representation of the entire cell-collagen environment. This method contains the analysis capabilities of the previous method but can include collagen data from stacks directly above and below the cell in its analysis.

Adviser: Guy Genin

Document Type

Final Report

Author's School

School of Engineering and Applied Science

Author's Department

Mechanical Engineering and Materials Science

Class Name

Mechanical Engineering and Material Sciences Independent Study

Date of Submission