RT Journal Article
SR Electronic
T1 3D-Cell-Annotator: an open-source active surface tool for single cell segmentation in 3D microscopy images
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 677294
DO 10.1101/677294
A1 Ervin A. Tasnadi
A1 Timea Toth
A1 Maria Kovacs
A1 Akos Diosdi
A1 Francesco Pampaloni
A1 Jozsef Molnar
A1 Filippo Piccinini
A1 Peter Horvath
YR 2019
UL http://biorxiv.org/content/early/2019/06/20/677294.abstract
AB Summary Segmentation of single cells in microscopy images is one of the major challenges in computational biology. It is the first step of most bioimage analysis tasks, and essential to create training sets for more advanced deep learning approaches. Here, we propose 3D-Cell-Annotator to solve this task using 3D active surfaces together with shape descriptors as prior information in a fully- and semi-automated fashion. The software uses the convenient 3D interface of the widely used Medical Imaging Interaction Toolkit (MITK). Results on 3D biological structures (e.g. spheroids, organoids, embryos) show that the precision of the segmentation reaches the level of a human expert.Availability and implementation 3D-Cell-Annotator is implemented in CUDA/C++ as a patch for the segmentation module of MITK. The 3D-Cell-Annotator enabled MITK distribution can be downloaded at: www.3D-cell-annotator.org. It works under Windows 64-bit systems and recent Linux distributions even on a consumer level laptop with a CUDA-enabled video card using recent NVIDIA drivers.Contacts filippo.piccinini{at}irst.emr.it and horvath.peter{at}brc.mta.hu