Jiaxiang Ren1, Zhenghong Li1, Wensheng Cheng1, Zhilin Zou1, Kicheon Park2, Yingtian Pan2, Haibin Ling1
1Department of Computer Science, 2Department of Biomedical Engineering
Stony Brook University
This repository is the official PyTorch implementation of 3D skeleton completion model.
pytorch == 1.12.1
scikit-image == 0.19.3
napari == 0.4.16
skan == 0.10.0
Ensure the trained model weight is in weights/model_weights_best.pth
. Then run the notebook inference_odt.ipynb
for inference.
-
MSD dataset can be downloaded from the official site. The annotation is in
dataset/MSD_annotation_3D.csv
. Note that only a part of original CT volumes contain vessels so we crop the volumes using the script indataset/task008_hvessel_preprocessing.ipynb
. The annotation is based on the cropped CT patches. -
10 ODT patches with [ODT image, mask, and skeleton] in
dataset/odt_testing.npy
are provided for 3D visualization. The whole ODT volomes used in this work is not available for now due to data policy.
This work was partially supported by NIH grants 1R21DA057699, 1RF1DA048808 and 2R01DA029718, and partially supported by NSF grants 2006665 and 2128350.