3D Cell Annotator software.

It consists of a CUDA implementation of the selective segmentation method (SelectiveSegmentation) and source code patch to the segmentation module of the MITK to interact with the CUDA implementation.

Build instructions:

1. Clone and checkout the 2018.04 version of MITK: https://github.com/MITK/MITK/tree/v2018.04 (commit ac93ed9baf)

   Make sure it can be built without errors using cmake and make.

2. Clone the 3DCellAnnotator source: git clone https://github.com/etasnadi/3DCellAnnotator.git

   1. cmake and make the SelectiveSegmentation project.

   2. cmake the MITKIntegration project. (Set the MITK_PATH variable to the root of the MITK source and PATCH_DIR to the MITKIntegration/mitk-patch directory in the 3DCellAnnotator source tree). In the build dir execute python patch.py apply (this project only intended to generate a python script that copies/updates the required code for the MITK interface of the SelectiveSegmentation project.

3. Go to the MITK-build directory under the MITK superbuild, and:

   Execute thecmakecommand again and set the Selective_DIR to the build directory of the SelectiveSegmentation using the cmake-gui or something on your system. Also, enable the MITK_BUILD_org.mitk.gui.qt.segmentation and MITK_BUILD_org.mitk.gui.qt.multilabelsegmentation checboxes to include the MITK's segmentation plugin in the build. make install.

   Copy the configuration file settings_3DCA.conf from the build dir of the SelectiveSegmentation project to the installed porject's bin directory.

The app can be executed using bin/MitkWorkbench.

See issue [#2] for a detailed example of how to build on Ubuntu 20.04!