Installation

The installation instructions are shown in Windows operation system. MacOS or Linux are not fully supported yet.

Sedeen Viewer

To use the plugins, you need to download Sedeen Viewer first.

Plugins and supporting files

Download our tools from Github page by clicking on the “Clone or download” button first and then clicking on the “Download ZIP” button.

If you have already installed Anaconda and set up the conda environment, please skip to Create environment variable.

Unzip cancer_diagnosis-master.zip, you will see the following folders:

• YNet: source code for YNet
• data: contains a sample test image
• models: contains pre-trained models
• output: output files for all modules (contains pre-computed features for sample image)
• utils: other supporting source code

The unzipped folder can either be named as “cancer_diagnosis” or “cancer_diagnosis-master”, which will not affect how the program runs.

Install Anaconda

You need to install Python and dependencies required to run the provided package. We use Anaconda to manage Python dependencies, and you can download the latest version of Anaconda with Python 3.7 or 3.8 from here .

You should follow the instructions as shown in the screenshots below. Pay attention to the buttons marked with red ink. Installing Anaconda for all users to the “C:/ProgramData/Anaconda3/” path can make the program running smoothly.

Install Dependencies

After installing Anaconda, you can install all the required packages by double clicking on the 0_install_dependencies.bat file, as shown below.

The installation may take around 10-20 minutes. After installation, you can proceed to tutorial.

If you see a “Windows protected your PC” window as below. You can first click on the “More Info” button and then “Run anyway” button to allow our program to run.

When the installation is done, you can see a similar message as shown below.

(Optional) Install CUDA for Nvidia GPU Only

In the semantic segmentation part, we will use Convolutional Neural Networks to analyze the input ROI images, and this slow process can be accelerated by using Nvidia GPUs. If you have an Nvidia GPU in your computer, you can download and install CUDA 10.2 before running our programs.

Supported Image Formats

We support PNG, JPG, TIFF, SVS, and many other image formats for MacOS and Linux. Unfortunately, we do not support SVS for Windows machine at the current stage, but you can easily convert your SVS files to JPG files by using this converter.

Create environment variable

1. Right-click the Computer icon and choose Properties, or in Windows Control Panel, choose System.
2. Choose Advanced system settings.

3. On the Advanced tab, click Environment Variables.

4. Click New under the User variables to create a new user variable.

Variable name: SedeenPythonHome
Variable value: "Full path of cancer_env"

Note that the path of cancer_env is usually *C:%Username%.conda_env. If you’re not sure where the conda env is, you can launch the command lines by Win+R*, open cmd, and run

conda env list

The path listed beside cancer_env is the value you should put in user variable.

5. Apply this change and reboot your computer.

Install Sedeen Plugins

Copy the folder ITCR to %Sedeen Viewer Folder%\plugins\cpp.

%Sedeen Viewer Folder% is where Sedeen is installed.

Now You can start using our plugins.