Mouse thorax segmentation dataset

<p>This repository contains reference segmentations of the heart, spinal cord, right lung and left lung for&nbsp;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.</p> <p>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:</p> <p>Malimban, J., Lathouwers, D., Qian, H.&nbsp;<em>et al.</em>&nbsp;Deep learning-based segmentation of the thorax in mouse micro-CT scans.&nbsp;<em>Sci Rep</em>&nbsp;12,&nbsp;1822 (2022). https://doi.org/10.1038/s41598-022-05868-7</p> <p>&nbsp;</p> <p>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&nbsp;</p>