Mouse thorax segmentation dataset

Zenodo (CERN European Organization for Nuclear Research)

Abstract

This repository contains reference segmentations of the heart, spinal cord, right lung and left lung for native and contrast-enhanced mouse CT images. The CTs were drawn from a publicly available preclinical micro-CT database1. Annotations are provided for the entire native CT dataset (140 images) and for a subset (35 images) of the contrast-enhanced CT dataset. Annotations by a second observer are also available for 35 native CTs and contrast-enhanced CTs. This dataset was used to train a nnU-Net 3d_fullres model for automated mouse thorax segmentation. The pre-trained model can be downloaded from https://doi.org/10.5281/zenodo.5786839 and more details about the dataset and training can be found in the publication. In case you find these annotations useful for your research, please cite the original work: Malimban, J., Lathouwers, D., Qian, H. et al. Deep learning-based segmentation of the thorax in mouse micro-CT scans. Sci Rep 12, 1822 (2022). https://doi.org/10.1038/s41598-022-05868-7 1Rosenhain S, Magnuska Z A, Yamoah G G, Rawashdeh W A, Kiessling F and Gremse F 2018 A preclinical micro-computed tomography database including 3D whole body organ segmentations Online: https://springernature.figshare.com/collections/A_preclinical_micro-computed_tomography_database_including_3D_whole_body_organ_segmentations/4224377/1

Authors 7

1. Justin Malimban

   University Medical Center Groningen

   Affiliation as printed

   Department of Radiation Oncology, University Medical Center Groningen

2. Danny Lathouwers

   Delft University of Technology

   Affiliation as printed

   Department of Radiation Science and Technology, Delft University of Technology

3. Haibin Qian

   Amsterdam UMC Location University of Amsterdam · Amsterdam University Medical Centers · Cancer Center Amsterdam

   Affiliation as printed

   Department of Medical Biology, Amsterdam University Medical Centers (Location AMC) and Cancer Center Amsterdam

4. Frank Verhaegen

   Maastricht University Medical Centre · Maastricht University

   Affiliation as printed

   Department of Radiation Oncology (MAASTRO), GROW School for Oncology and Developmental Biology, Maastricht University Medical Center

5. Julia Wiedemann

   University Medical Center Groningen

   Affiliation as printed

   Department of Radiation Oncology, University Medical Center Groningen

6. Sytze Brandenburg

   University Medical Center Groningen

   Affiliation as printed

   Department of Radiation Oncology, University Medical Center Groningen

7. Marius Staring Aachen Department of Radiology, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Department of Radiology, Leiden University Medical Center