Platelet analysis

This code implements the methods proposed in the following paper:

[1] Johanna C. Clauser, Judith Maas, Jutta Arens Thomas Schmitz-Rode, Ulrich Steinseifer, and Benjamin Berkels. Automation of Hemocompatibility Analysis Using Image Segmentation and Supervised Classification. Engineering Applications of Artificial Intelligence, 97, January 2021. [DOI | arXiv]

It is based on the QuocMesh software library, AG Rumpf, Institute for Numerical Simulation, University of Bonn, and distributed under the terms of the Common Development and Distribution License. Particularly, you can download and use this software free of cost.

Some subdirectories contain code from other software projects, which is redistributed under the respective licenses:

• quocmesh/external/bz2/

  Code from the bzip2 library by Julian R Seward, License under external/bz2/LICENSE

• quocmesh/external/dirent/dirent.h

  Code from the Dirent API by Toni Ronkko, License at the beginning of external/dirent/dirent.h

• quocmesh/cmake/FindSUITESPARSE.cmake

  CMake module from OpenFlipper, GNU Lesser General Public License

We appreciate any feedback on your experience with our methods. In case you encounter any problems when using this software, please do not hesitate to contact us: [email protected]

Prerequisites

To build the software, cmake and a compiler like GCC or clang need to be installed. Furthermore, a few external libraries are needed. Under Linux, usually all of the dependencies can be installed with the package manager that comes with the Linux distribution. Under OS X/macOS, the installation of a third party package manager like MacPorts or Homebrew is recommended. For instance, if MacPorts is installed, one can install cmake with:

sudo port install cmake

Compiling

First create a clone of our git repository e.g. by

git clone https://github.com/berkels/platelet-analysis

In the clone directory, there should be two directories, quocmesh and quocGCC. The source code is in quocmesh, the compiled binaries will go into quocGCC.

To compile the code, go into the directory quocGCC and call the script called goLinux.sh (or goWindows.bat if compiling under Windows with MinGW). This invokes cmake with all necessary options and will create makefiles.

After the go script has been run, the source can be compiled with make like any other project with makefiles. There is also a test target to check whether the basics of the code actually work.

In short, to get started the following steps should be enough: Decompress the archive and change into the directory quocGCC. In there, call

./goLinux.sh
make
make test

Under Windows with MinGW call

./goWindows.bat
mingw32-make
mingw32-make test

instead.

If all dependencies are installed correctly, this should work without any errors (although there may be warnings during the first two steps).

To speed up the compilation, one can have make use as many threads as desired, by calling make -jN (where N is the number of threads) instead of just make.

Running

TODO

Note: So far this repository only contains the segmentation code. The remaining parts will be added soon.