Detection of Lung Nodules in Micro-CT Imaging Using Deep Learning
Matthew D. Holbrook; Darin P. Clark; Rutulkumar Patel; Yi Qi; Alex M. Bassil; Yvonne M. Mowery; Cristian T. Badea
Tomography 2021, Volume 7, Issue 3, 358-372
Data and Code Availability: The data presented in this work are available by request at https://civmvoxport.vm.duke.edu, and the code used for training and analysis can be found at https://github.com/mdholbrook/lung-tumor-detection.
Our tumor mapping paper is now published and our images made the cover:
Blocker SJ et al. Ex Vivo MR Histology and Cytometric Feature Mapping Connect Three-dimensional in Vivo MR Images to Two-dimensional Histopathologic Images of Murine Sarcomas.
Radiol Imaging Cancer 2021 May;3(3):e200103. doi: 10.1148/rycan.2021200103
Our p53/MCA High Mutational Load Model of Soft Tissue Sarcoma
Dr. Yvonne Mowery
To recapitulate human soft tissue sarcoma (STS) in the preclinical setting of our co-clinical trial, we generate a primary mouse model of STS by intramascular injection of adenovirus containing Cas9 gene and a guide RNA targeting p53 gene (Adeno-Cas9-sgRNAp53) and carcinogen 3-methylcholanthrene (MCA) into the gastrocnemius muscle of wild-type 129/SvJ mice. This is describe in:
Primary Sarcoma Model Protocols – Ad-Cre or Ad-sgp53-Cas9 Intramuscular Injection
Co-Clinical Imaging Resource Program (CIRP): Bridging the Translational Divide to Advance Precision Medicine. Tomography. 2020 Sep;6(3):273-287. doi: 10.18383/j.tom.2020.00023.
We have created an image processing pipeline for high-throughput, reduced-bias segmentation of multiparametric tumor MRI data and radiomics analysis, to better our understanding of preclinical imaging and the insights it provides when studying new cancer therapies.
Link to our new paper
As part of our co-clinical trial studying immunotherapy and radiotherapy in sarcomas, we are using micro-CT of the lungs to detect and measure metastases as a metric of disease progression. In this study, we have addressed the impact of respiratory gating during micro-CT acquisition on improving lung tumor detection and volume quantitation.
S. J. Blocker,M. D. Holbrook,Y. M. Mowery,D. C. Sullivan,C. T. Badea, The impact of respiratory gating on improving volume measurement of murine lung tumors in micro-CT imaging, https://doi.org/10.1371/journal.pone.0225019
This is a MATLAB-based tool for converting 3D CT image volumes from NifTi format to DICOMs. This repository contains a GUI which can be used to assign values to common DICOM fields. It also contains functions which can be used in your own code to streamline workflows.
Generalized Scanning Protocol (U24) – SOP
This SOP is designed as a general guide for in vivo MR imaging of small animals as part of a pre-clinical cancer study, using a volume transmit coil + surface receive coil at high fields. Note that this protocol begins with information that is not machine or project specific.
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