Category Archives: Uncategorized

Leveraging 3D Bioprinting & Photon-Counting Computed Tomography for Regenerative Medicine

An exciting publication on our collaborative research focusing on the innovative applications of 3D Bioprinting and Photon-Counting CT.

Gil CJ, Evans CJ, Li L, Allphin AJ, Tomov ML, Jin L, Vargas M, Hwang B, Wang J, Putaturo V, Kabboul G, Alam AS, Nandwani RK, Wu Y, Sushmit A, Fulton T, Shen M, Kaiser JM, Ning L, Veneziano R, Willet N, Wang G, Drissi H, Weeks ER, Bauser-Heaton HD, Badea CT, Roeder RK, Serpooshan V. Leveraging 3d Bioprinting And Photon-Counting Computed Tomography to Enable Noninvasive Quantitative Tracking of Multifunctional Tissue Engineered Constructs. Adv Healthc Mater. 2023 Sep 14:e2302271. doi: 10.1002/adhm.202302271. PMID: 37709282.

Read the full paper here

A big thank you to our team and collaborators..

Deep Learning Denoising for Photon-Counting CT

Nadkarni, R.; Clark, D.P.; Allphin, A.J.; Badea, C.T. A Deep Learning Approach for Rapid and Generalizable Denoising of Photon-Counting Micro-CT Images. Tomography 20239, 1286-1302.

MCR toolkit

Our QIAL developed Multi-Channel CT Reconstruction (MCR) Toolkit addresses unique challenges associated with in vivo preclinical micro-CT and supporting the translation of these advancements to the clinical domain.

We have now published a paper in Medical Physics detailing our toolkit’s capabilities and functions:

Clark DP, Badea CT. MCR toolkit: A GPU-based toolkit for multi-channel reconstruction of preclinical and clinical x-ray CT data. Med. Phys.. 2023;1-22. 

Co-Clinical Imaging

Our group contributed to these new papers from the co-clinical imaging research program (CIRP) :

1.Moore, S.M.; Quirk, J.D.; Lassiter, A.W.; Laforest, R.; Ayers, G.D.; Badea, C.T.; Fedorov, A.Y.; Kinahan, P.E.; Holbrook, M.; Larson, P.E.Z.; Sriram, R.; Chenevert, T.L.; Malyarenko, D.; Kurhanewicz, J.; Houghton, A.M.; Ross, B.D.; Pickup, S.; Gee, J.C.; Zhou, R.; Gammon, S.T.; Manning, H.C.; Roudi, R.; Daldrup-Link, H.E.; Lewis, M.T.; Rubin, D.L.; Yankeelov, T.E.; Shoghi, K.I. Co-Clinical Imaging Metadata Information (CIMI) for Cancer Research to Promote Open Science, Standardization, and Reproducibility in Preclinical ImagingTomography 20239, 995-1009.

2.Gammon, S.T.; Cohen, A.S.; Lehnert, A.L.; Sullivan, D.C.; Malyarenko, D.; Manning, H.C.; Hormuth, D.A.; Daldrup-Link, H.E.; An, H.; Quirk, J.D.; Shoghi, K.; Pagel, M.D.; Kinahan, P.E.; Miyaoka, R.S.; Houghton, A.M.; Lewis, M.T.; Larson, P.; Sriram, R.; Blocker, S.J.; Pickup, S.; Badea, A.; Badea, C.T.; Yankeelov, T.E.; Chenevert, T.L. An Online Repository for Pre-Clinical Imaging Protocols (PIPs)Tomography 20239, 750-758.


QIAL papers at SPIE Medical Imaging 2023

1)  A Allphin, R Nadkarni, D Clark, C T Badea. Ex vivo high-resolution hybrid micro-CT imaging using photon counting and energy integrating detectors. Proc. of SPIE Vol 12468, 124680V-1, 2023

2) DP Clark, FR Schwartz, A Euler, V Mergen, H Alkadhi, D Marin, CT Badea  Unsupervised learning of robust models for cardiac and photon-counting x-ray CT denoising, SPIE Medical Imaging 2023: Physics of Medical Imaging 12463, 329-337

3) AJ Allphin, DP Clark, T Thuering, P Bhandari, KB Ghaghada, CT Badea Spectral micro-CT imaging of multiple K-edge elements using GaAs and CdTe photon counting detectors, SPIE Medical Imaging 2023: Physics of Medical Imaging 12463, 153-159

Spectral CT imaging using GaAs and CdTe photon counting detectors

In this study, we compared the performance of PC micro-CT imaging when using two types of PCDs. We have also demonstrated the ability of PCDs to separate a wide range of K-edge materials.

Alex Jeffrey Allphin, Darin P Clark, Thomas Thüring, Prajwal Bhandari, Ketan B Ghaghada, Cristian T Badea. Micro-CT imaging of multiple K-edge elements using GaAs and CdTe photon counting detectors. Physics in Medicine & Biology, 2023, DOI 10.1088/1361-6560/acc77e

Group Photo

QIAL members and the Bass Connections team, March 2023

Artist and T-shirts Designer: Nariman (Ali) Mahzarnia


Animal Models and Their Role in Imaging-Assisted Co-Clinical Trials

This overview paper describes the ten co-clinical trials of investigators from eleven institutions who are supported by the CIRP initiative and are members of the Animal Models and Co-clinical Trials (AMCT) Working Group.

Examples of MRI and micro-CT images in the p53/MCA model and the schematics of the preclinical arm of the clinical trial organized at Duke.

Peehl, D.M.; Badea, C.T.; Chenevert, T.L.; Daldrup-Link, H.E.; Ding, L.; Dobrolecki, L.E.; Houghton, A.M.; Kinahan, P.E.; Kurhanewicz, J.; Lewis, M.T.; Li, S.; Luker, G.D.; Ma, C.X.; Manning, H.C.; Mowery, Y.M.; O’Dwyer, P.J.; Pautler, R.G.; Rosen, M.A.; Roudi, R.; Ross, B.D.; Shoghi, K.I.; Sriram, R.; Talpaz, M.; Wahl, R.L.; Zhou, R. Animal Models and Their Role in Imaging-Assisted Co-Clinical TrialsTomography 20239, 657-680.

QIAL papers @ CT Meeting 2022

1. C. Badea, D. Clark, A. Alphin, J. C. Ramirez-Giraldo, P. Bhandari, Y. Mowery, K. Ghaghada. Co-clinical photon counting CT research for multi-contrast imaging. Proceedings Volume 12304, 7th International Conference on Image Formation in X-Ray Computed Tomography; 123040G (2022)
2. Darin P. Clark, Alex J. Allphin, Yvonne M. Mowery, Cristian T. Badea. Photon-counting x-ray CT perfusion imaging in animal models of cancer . Proceedings Volume 7th International Conference on Image Formation in X-Ray Computed Tomography, 123041B (2022)
3. Rohan Nadkarni, Alex Allphin, Darin Clark, Cristian Badea. Material decomposition from photon-counting CT using a convolutional neural network and energy-integrating CT training labels.  Proceedings Volume 12304, 7th International Conference on Image Formation in X-Ray Computed Tomography; 123041K (2022))

Preclinical implementation of a clinical trial

This study aimed to investigate whether adding neoadjuvant radiotherapy (RT), anti-programmed cell death protein-1 (PD-1) antibody (anti-PD-1), or RT + anti-PD-1 to surgical resection improves disease-free survival for mice with soft tissue sarcomas (STS). The paper has been included in the highlights.