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FastPathology

FastPathology is an open-source platform for deep learning-based research and decision support in digital pathology, created by SINTEF Medical Technology and the Norwegian University of Science and Technology (NTNU).

Install

Download an appropriate installer from the release page. Installers for Win10 and Ubuntu (18 and 20) are available.

NOTE: FastPathology depends on OpenCL. Most Windows machines have OpenCL by default, whereas Ubuntu does not. Thus, for Ubuntu, OpenCL can be installed by installing either NVIDIA CUDA Toolkit or Intel OpenCL SDK. For both operating systems CUDA is required to run inference on a dedicated GPU.

Test data

Data for testing the application can be downloaded from here. It includes some pretrained models, two WSIs, and some example text pipelines. If curl and tar is installed on the machine (works for both Ubuntu and Windows), it is now possible to download the data directly from the GUI (go to the menu bar -> Edit -> Download test data -> click "Yes" -> when finished, click "Yes" again to visualize the WSIs straight away).

Features

The software is implemented in C++ based on FAST. A wide range of features have been added to the platform and FAST to make working with Whole Slide Images (WSIs) a piece of cake!

• Graphical User Interface - User-friendly GUI for working with WSIs without any code interaction
• Deep learning - Deployment and support for multi-input/output Convolutional Neural Networks (CNNs)
• Visualization - Real-time streaming of predictions on top of the WSI with low memory cost
• Use cases - Patch-wise classification, low and high-resolution segmentation, and object detection are supported
• Inference Engines - FAST includes a variety of different inference engines, e.g. TensorFlow CUDA, TensorRT and OpenVINO.
• Text pipelines - Possibility to create your own pipelines using the built-in script editor
• Formats - Through OpenSlide FastPathology supports lots of WSI formats

Demos

Very simple demonstrations of the platforms can be found on Youtube. Tutorials and more in-depth demonstrations will be added in the future.

Development setup

1. Either
   • Download a release of FAST and install its requirements.
   • Compile and install FAST on your system: See instructions here for Windows or Linux (Ubuntu).
2. Clone this repository

   git clone https://github.com/SINTEFMedtek/FAST-Pathology.git

3. Setup build environment using CMake
   Linux (Ubuntu)

   mkdir build
   cd build
   cmake .. -DFAST_DIR=/path/to/FAST/cmake/

   Windows (Visual Studio) Modify generator -G string to match your Visual studio version. This command will create a visual studio solution in your build folder.

   mkdir build
   cd build
   cmake .. -DFAST_DIR=C:\path\to\FAST\cmake\ -G "Visual Studio 16 2019" -A x64

4. Build

   cmake --build . --config Release --target fastpathology

5. Run Linux (Ubuntu)

   ./fastpathology

   Windows

   cd Release
   fastpathology.exe

NOTE: Both VS 17 and 19 have been tested with both FAST and FastPathology and works well.