Analyzing angiogenesis on a chip using deep learning-based image processing

Source code for my publication,<Analyzing angiogenesis on a chip using deep learning-based image processing> https://pubs.rsc.org/en/content/articlehtml/2023/lc/d2lc00983h

!! This code implemented the NuSet, https://github.com/yanglf1121/NuSeT For Nuclei segmentation process. I want to show my deepest appreciation to the authors of NuSeT, https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008193

Installation :

Download files or clone this git.
At your python terminal, please install all required modules by entering followings:

  pip install -r requirements.txt

!Important!

This application is optimized for following versions of modules :

python : 3.7.0
tensorflow-gpu:1.15.0
numpy:1.19.0

If error occurs during installation, please refer the git of yanglf1121.

Also, PLEASE MAKE SURE THAT THE IMAGE YOU WANT TO ANALYZE HAS NUCLEI INFORMATION ON BLUE CHANNEL, AND VASCULAR INFORMATION ON GREEN AND RED CHANNEL.

Press'Analyze Image' button and wait for a while.
If you see 'Fill' window, it means that the process is done.
Check the newly founded csv file and directory. The name of file/dir is decided by the time you run this application.

Name		Name	Last commit message	Last commit date
Latest commit History 7 Commits
model_layers		model_layers
utils		utils
.gitignore		.gitignore
LICENSE		LICENSE
NuSeT.py		NuSeT.py
NuSeT_CL.py		NuSeT_CL.py
README.md		README.md
edge_property.py		edge_property.py
img_process.py		img_process.py
main_ui.py		main_ui.py
node_property.py		node_property.py
pyvenv.cfg		pyvenv.cfg
requirements.txt		requirements.txt
sample.tif		sample.tif
sample_data.csv		sample_data.csv
test.py		test.py

moonchildz/angio_analysis