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Quantify tissue damage with ML

License: MIT License

MATLAB 100.00%

lungdamage's Introduction

LungDamage

Quantify tissue damage with ML

Contact and Referencing

Any comments or questions can be directed to: Will Liberti at [email protected]

If you use this in your work, please cite:

Alveolar epithelial cell fate is maintained in a spatially restricted manner to promote lung regeneration after acute injury, Liberti et al.

Requirements:

Before you begin, make sure you have the following MATLAB toolboxes installed:

Basic Walkthrough

Take this example image:

>> % cd('images'); enter the images directory

>> RGB1 = DL_demo % load 'image00.jpg'

Isolate the moderately damaged tissue:

Isolate just the severely damaged tissue:

Clustering multipe images

Sometimes you will want to cluster several images, or cluster relative to a known healthy, or known damaged reference sample.

>> % cd('images/Unprocessed')
>> out = DL_demo_ref('S.jpg')

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lungdamage's Issues

Reference to undamaged tissue

Pass undamaged tissue image to act as a reference for the damaged tissue.

public repository

Host some of the data in a public repo accessible by FTP, to reduce the size of the codebase

Typo in DL_demo_ref

% concatonate Images should be % concatenate images

Show cluster without demarcation?

Can we show a print of the clustering itself with no demarcations? I think this got deleted in the last update.

Updates

Finalize damage program for submission
Separate counting from damage program
Segregate clustering validation from damage program demo run

add hierarchical clustering to validate K-means

Batch processing and quantification

Add batch processing for multiple samples, save processed images and add statistical quantification.

Limit to 3 graphs

Looks like only up to 3 graphs will output on a give run of an image folder, is there a way for graphs to scale with image files run?

Xmass_tish update

Xmass_tish line 1: change xmass_song to xmass tish
Xmass_tish line 29: should read baseline to baseline

ROI

Is there a way to export the demarcation annotation as a mask or ROI that can be imported into fiji or overlayed ontop of another image?

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