REAL

3D-Cell-Annotator: an open-source active surface tool for single-cell segmentation in 3D microscopy images

Tasnádi, Ervin A. and Tóth, Tímea and Kovács, Mária and Diósdi, Ákos and Pampaloni, Francesco and Molnár, József and Horváth, Péter (2020) 3D-Cell-Annotator: an open-source active surface tool for single-cell segmentation in 3D microscopy images. BIOINFORMATICS, 36 (9). pp. 2948-2949. ISSN 1367-4803

[img]
Preview
Text
btaa029.pdf

Download (257kB) | Preview

Abstract

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 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.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.Supplementary data are available at Bioinformatics online.

Item Type: Article
Additional Information: Synthetic and System Biology Unit, Biological Research Centre (BRC), Szeged, H-6726, Hungary Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University of Frankfurt, Frankfurt, DE-60438, Germany Istituto Scientifico Romagnolo per Lo Studio e la Cura Dei Tumori (IRST) IRCCS, Meldola (FC), I-47014, Italy Institute for Molecular Medicine Finland University of Helsinki, Helsinki, FI-00014, Finland Single-Cell Technologies Ltd, Szeged, H-6726, Hungary Cited By :1 Export Date: 16 September 2020 CODEN: BOINF Correspondence Address: Horvath, P.; Synthetic and System Biology Unit, Biological Research Centre (BRC), Istituto Scientifico Romagnolo per Lo Studio e la Cura Dei Tumori (IRST) IRCCS, Institute for Molecular Medicine Finland University of Helsinki, Single-Cell Technologies LtdHungary; email: horvath.peter@brc.hu
Subjects: Q Science / természettudomány > QH Natural history / természetrajz > QH301 Biology / biológia
SWORD Depositor: MTMT SWORD
Depositing User: MTMT SWORD
Date Deposited: 29 Jan 2021 10:38
Last Modified: 29 Jan 2021 10:38
URI: http://real.mtak.hu/id/eprint/120216

Actions (login required)

Edit Item Edit Item