Myofibrometry

Welcome to the myofibrometry project. Follow all the detailed steps described in README.md in sequence. After you follow all steps you will have one sample dataset called SAS3 in the data/ sub-folder and streamline generation scripts in the visualization/heart_vis sub-folder and plots and images in the results/ folder. The source matlab code for generating these results is in the matlab/ folder and requires Matlab to run. After running the matlab scripts, the data/ folder will contain .mat files which can be used as inputs for visualizing streamlines using the blender scripts in the visualization/heart_vis sub-folder. Detailed instructions on running the blender scripts will be in the README.md file in the visualization/heart_vis sub_folder.

Carry out the following sequence of steps to reproduce the results:

[1] Clone This Repository

To clone this repository first git clone this repository and install all submodules of the repository.

$ git clone https://gitfront.io/r/myoarch/fZmkh5iHEJae/myofibrometry.git
$ cd myofibrometry
$ bash install.sh

[2] Download Dataset

To download the image dataset run the data download script inside the main folder.

$ cd myofibrometry
$ chmod +x download.sh
$ ./download.sh

If the download finishes successfully, you should see a sub folder SAS3 inside the data folder containing two tif files, wga.tif and denoised.tif. The download time will depend on your internet connection.

[3] Generate Field Files

This and the following step should be run using Matlab. The code requires atleast matlab-2021. However, you manage with version 2019 if you skip saving the final generated plots.

After launching Matlab enter the matlab folder and run the startup script. This script sets up the proper paths required to run the subsequent scripts.

>> startup

Field files can be generated by running the generateOrientationFields Matlab script.

>> generateOrientationFields

For this script to run successfully your machine should have least around 128 GB RAM. This script may take a while to run, so it is best run it overnight. Once successfully run your SAS3 sub folder should contain two new mat files. Specifically, it should now contain two files named field2d.mat and field_sigma_4.mat.

[4] Generate Helix Angle plots

To reproduce helix angle plots for different sectors run the generateSectorPlots script

>> generateSectorPlots

The script should run within a few minutes and save the generated figures inside the results folder.

Enjoy looking at the plots!