Cancer 3D multicellular spheroid segmented in single cells
3D-CELL-ANNOTATOR, A MITK PLUGIN:
3D-Cell-Annotator is a patch for the segmentation plugin of the Medical Imaging Interaction Toolkit version 2018.04 (MITK, http://docs.mitk.org/nightly/) written in C++/CUDA and distributed as a full MITK distribution, however building from source is also possible. 3D-Cell-Annotator works on Windows and Linux operating systems. It requires a CUDA-enabled Graphic Processing Unit (GPU) and a recent version of NVidia driver (Linux: 410.104; Win: 411.31). For normal usage a mid-category GPU with several hundreds of processing threads (CUDA cores) is required, such as GeForce 850M or above. The software needs 9 bytes of memory per voxel on the GPU at peak load, therefore a ~750 by 750 by 750 image can be processed with a GPU with 4GB RAM.
DESCRIPTION OF THE MATHEMATICAL MODEL IMPLEMENTED:
In the PDF file here available it is possible to find a rigorous mathematical description of the implemented model:
-> Download
USER MANUAL:
The Grapical User Interface (GUI) of 3D-Cell-Annotator is complex, but robust. You will need some time to become familiar with that. This user manual and the Sample Dataset provided in the Download Section of this webite can help you to speed-up the process.
-> Download
VIDEO TUTORIAL 01: "GETTING STARTED":
This video tutorial shows how 3D-Cell-Annotator works and what its basic features are.
