/Nuclei_Segmentation

This is the source code for training and testing our three class CNN algorithm for generalized nuclei segmentation (IEEE TMI paper) using Torch.

Primary LanguageLua

Nuclei Segmentation

Following are the instructions to test our state-of-the art deep learning based nuclei segmentation software using an AWS EC2 instance-

Step 1

Create an instance and configure it for using CUDA enabled Torch (refer to https://drive.google.com/file/d/0ByERBiBsEbuTUS0wdWQ2NUZGTm8/view)

Step 2

Get the software from Github

git clone https://github.com/neerajkumarvaid/NucleiSegmentation

Step 3

Test our state-of-the art nuclei segmentation model

cd NucleiSegmentation

th predict_full_mask.lua

Results will be saved in the /data/testing-data/40x/results folder

Step 4

Zip the results folder and download in your laptop's "Downloads" folder

zip -r results.zip results

scp –i key.pem user@ip:~/NucleiSegmentation/data/testing-data/40x/results.zip ~/Downloads/

This will give you three images from CNN output 1.png, 2.png and 3.png. Please refer to nucleisegmentationbenchmark.weebly.com for post-processing and model details.

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