‘Deep Learning’

Overview of our proposed pre-training framework.
Input CT images are randomly cropped into sub-volumes and
augmented with random inner cutout and rotation, then fed to the
Swin UNETR encoder as input. We use masked volume inpainting,
contrastive learning and rotation prediction as proxy tasks for
learning contextual representations of input images

Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis

Jul. 25, 2022—Tang, Yucheng, Dong Yang, Wenqi Li, Holger R. Roth, Bennett Landman, Daguang Xu, Vishwesh Nath, and Ali Hatamizadeh. “Self-supervised pre-training of swin transformers for 3d medical image analysis.” In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, pp. 20730-20740. 2022. Full text: Abstract Vision Transformers (ViT)s have shown great performance in self-supervised...

Representative images are predicted to associate with comorbidities and ICD-10 codes
(phenotype components) identified in each risk category. The red outlines show the pancreas
tissue can be different under phenotyping contexts. (1) is from a nominally healthy pancreas
group with potential lung infections; (2) is from type I diabetes and other chronic kidney disease
patients with atrophic pancreas; (3) is from other metabolic syndromes including type II diabetes;
(4) is from patients with weight loss and pancreatitis.

Pancreas CT Segmentation by Predictive Phenotyping

Dec. 14, 2021—Y. Tang, R.Gao, H.H.Lee, Q.Yang, X.Yu,Y.Zhou, S.Bao, Y.Huo, J.Spraggins, J.Virostko, Z.Xu, B.A. Landman. “Pancreas CTSegmentation by Predictive Phenotyping”. International Conference on MedicalImage Computing and Computer Assisted Intervention(MICCAI), 2021 Full Text: https://link.springer.com/chapter/10.1007/978-3-030-87193-2_3 Abstract Pancreas CT segmentation offers promise at understanding the structural manifestation of metabolic conditions. To date, the medical primary record of conditions that impact...

Method framework. Given a CT scan with at high resolution of ~0.8 x ~0.8 x ~2 mm, a low-res section (left panel) is trained with multi-channel segmentation. The low-res part contains down-sampling and normalization in order to preserve the complete spatial information. After the coarse segmentations are acquired from low- res UNet, we interpolate the mask to match the image’s original resolution. Next, random patch sampling (mid panel) is employed to collect patches, and patches are concatenated with corresponding coarse segmentation masks. Finally, we trained a patch-based high-res (right panel) segmentation model, the high-dimensional probability maps are acquired from integration of all patches on field of views. Majority vote is used to merge estimates into a final segmentation.

High-resolution 3D abdominal segmentation with random patch network fusion

Dec. 14, 2021—Y. Tang,R.Gao,S.Han, Y.Chen, D.Gao, V.Nath, C.Bermudez, M.R. Savona, R.G. Abramson, S.Bao,I.Lyu, Y.Huo and B.A. Landman,“High-resolution 3D Abdominal Segmentation with Random PatchNetworkFusion”,Medical Image Analysis, 2021. Full Text: https://www.sciencedirect.com/science/article/pii/S1361841520302589 Abstract Deep learning for three dimensional (3D) abdominal organ segmentation on high-resolution computed to- mography (CT) is a challenging topic, in part due to the limited memory provide...

A comparison of the number of learnable parameters and the types and number of skip connections in our five models. Note that the skip connections type column lists operations which show how residual information is reintegrated when the skip / residual connection or parallel processing branch rejoins the network.

Technical Note: Comparison of Convolutional Neural Networks for Detecting Large Vessel Occlusion on Computed Tomography Angiography

Jul. 21, 2021—Lucas W. Remedios, Sneha Lingam, Samuel W. Remedios, Riqiang Gao, Stephen W. Clark, Larry T. Davis, Bennett A. Landman. Technical Note: Comparison of Convolutional Neural Networks for Detecting Large Vessel Occlusion on Computed Tomography Angiography. Medical Physics, 2021 Full Text Abstract Purpose: Artificial intelligence diagnosis and triage of large vessel occlusion may quicken clinical response for...

Learning from dispersed manual annotations with an optimized data weighting policy

Dec. 7, 2020—Yucheng Tang, Riqiang Gao, Yunqiang Chen, Dashan Gao, Michael R. Savona, Richard G. Abramson, Shunxing Bao, Yuankai Huo and Bennett A. Landman, “Learning from Dispersed Manual Annotations with an Optimized Data Weighting Policy”, Journal of Medical Imaging, 2020. Full Text: Abstract https://pubmed.ncbi.nlm.nih.gov/32775501/ Purpose: Deep learning methods have become essential tools for quantitative interpretation of medical...

Figure 1. Renal structures segmentation of clinically acquired CT image. Yellow box shows a representative right kidney, green box shows the left kidney. The zoom-in patches show the CT kidney field-of-view (FOV) and labels. The label patches display the renal cortex (blue), the medulla (red) and the pelvicalyceal system (green). Those small structures make automatic renal segmentation challenging.

Renal Cortex, Medulla and Pelvicaliceal System Segmentation on Arterial Phase CT Images with Random Patch-based Networks

Nov. 21, 2020—Yucheng Tang, Riqiang Gao, Ho Hin Lee, Brent V. Savoie, Shunxing Bao, Yuankai Huo, Jeffrey Spraggins and Bennett A, Landman, Renal Cortex, Medulla, Pelvis Segmentation on Arterial Phase CT Images with Random Patch-based Networks, SPIE 2021 Medical Imaging Full Text Abstract Renal segmentation on contrast-enhanced computed tomography (CT) provides distinct spatial context and morphology. Current studies for renal segmentations...

Montage based 3D Medical Image Retrieval from Traumatic Brain Injury Cohort using Deep Convolutional Neural Network

Dec. 10, 2018—Cailey I. Kerley, Yuankai Huo, Shikha Chaganti, Shunxing Bao, Mayur B. Patel, Bennett A. Landman. “Montage based 3D Medical Image Retrieval from Traumatic Brain Injury Cohort using Deep Convolutional Neural Network.” In SPIE Medical Imaging, International Society for Optics and Photonics, 2019. Full text: NIHMSID Abstract Brain imaging analysis on clinically acquired computed tomography (CT) is essential...