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This is the source code for training and testing a three class CNN for nuclei segmentation using Torch

Shell 8.37% Python 15.86% Lua 75.77%

nucleisegmentation's Introduction

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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weihaoxie / nucleisegmentation Goto Github PK