johnmarianhoffman.github.io

John Hoffman

About

Websites

• https://github.com/johnmarianhoffman/
• https://github.com/freect

Academic studies

• Ph.D. Biomedical Physics, UCLA, Los Angeles, CA (2018) (dissertation)
• B.S. Mathematics, Virginia Tech, Blacksburg, BA (2011)
• B.S. Physics, Virginia Tech, Blacksburg, BA (2011)

Experience

• Computer Vision Engineer focusing on 3D Reconstruction, Magic Leap, December 2018 - Present
  • Specialized in improving robustness of segmentation algorithms for multi-view surface capture
  • Developed a surface registration pipeline based on deformation graphs to temporally register surfaces for compression of 3D data
  • Implemented sophisticated texture atlassing software for mapping 3D surfaces into 2D
• Independent Contractor, iTomography, December 2017 - May 2019
  • Concentrated on GPU acceleration of CT reconstruction software
• Post-Doctoral Researcher, UCLA Radiology, April 2018 - October 2018
• Graduate Student Researcher, UCLA Biomedical Physics Interdepartmental Program, June 2011 - March 2018
• Imaging Scientist, Toshiba Medical Research USA, Inc., October 2016 - December 2017

Research Interests

My research interests include 3D image and surface reconstruction, quantitative imaging and computer vision, and computational geometry. Additionally, I aim to incorporate automation, high-performance, and parallel computing into my research workflows to accelerate the amount of data we are able to consider and generate.

Publications

• (In preparation) Hoffman, J., Kim, G., Young, S., McNitt-Gray, M. Evaluating the Effects of a Range of Acquisition and Reconstruction Parameters on a Quantitative CT Imaging Task: Application of the Pipeline to Evaluate Quantitative Measures of Emphysema in a Large Lung Screening Cohort. (2020).

• (link) Hsieh, Scott S., Hoffman, John M., Noo, F. Accelerating Iterative Coordinate Descent Using a Stored System Matrix. Medical Physics 46(12), e801-e809 (2019).

• (link) Hoffman, J., Kim, G., Young, S., McNitt-Gray, M. Technical Note: Design and Implementation of a High Throughput Pipeline for Reconstruction and Quantitative Analysis of CT Image Data”. Medical Physics, 46(5), 2310-2322 (2019).

• (link) Zhao, T., Hoffman, J., McNitt-Gray, M., Ruan, D. Ultra-low-dose CT image denoising using modified BM3D scheme tailored to data statistics. Medical Physics, 46(1), 190-198 (2018).

• (link) Hoffman, J. , Noo, F.1, Young, S.1, Hsieh, S., McNitt-Gray, M. Technical Note: FreeCT_ICD: An Open Source Implementation of a Model-Based Iterative Reconstruction Method Using Coordinate-Descent Optimization for CT Imaging Investigations. Medical Physics, 45(8), 3591-3603, (2018)

• (link) T. Martin, J. Hoffman, J.R. Alger, M. Mcnitt-Gray, and D.J. Wang, Low-dose CT perfusion with projection view sharing. Medical Physics, 45(1), 101–113 (2017).

• (link) Young, S., Lo, P., Kim, G., Brown, M., Hoffman, J., Hsu, W., … McNitt-Gray, M. The Effect of Radiation Dose Reduction on Computer-Aided Detection (CAD) Performance in a Low-Dose Lung Cancer Screening Population. Medical Physics, 44(4), 1337–1346, (2017).

• (link) Hoffman, J., Young, S., Noo, F., & McNitt-Gray, M. Technical Note: FreeCT_wFBP: A Robust, Efficient, Open-Source Implementation of Weighted Filtered Backprojection for Helical, Fan-Beam CT. Medical Physics, 43, 10 pp., (2016).

Presentations

• (slides) “Imaging Is a Numbers Game: Challenges and Breakthroughs in CT Quantitative Imaging.” Imaging Elevated: Utah Symposium for Emerging Investigators. September 29-30, 2017. University of Utah, Salt Lake City UT.

• “High Throughput Computing in Quantitative CT Imaging: Development and Applications.” PKU-UCLA Joint Research Institute in Science and Engineering. 8th Annual Symposium. June 29-30, 2017. Peking University, Beijing, China.

Abstracts

• (slides) Hoffman, J., Hsieh, S., Kim, G.H., Brown, M., Goldin, J., McNitt-Gray, M. Simple Image Domain Denoising with An Adaptive Bilateral Filter Drastically Improves the Robustness of Quantitative Emphysema Scoring to Changes in Dose, Reconstruction Kernel, and Slice Thickness. 2018 AAPM Annual Meeting, Nashville, TN. (August, 2018).
• Zhao, T., Hoffman, J., McNitt-Gray, M., Ruan, D. Application and Performance Evaluation of a Modified BM3D Denoising Method to Emphysema Scoring On Ultra-Low-Dose CT Images. 2018 AAPM Annual Meeting, Nashville, TN. (August, 2018).
• Wahi-Anwar, M., Emaminejad, N., Hoffman, J., Kim, G.H., Brown, M., McNitt-Gray, M. Towards Quantitative Imaging: Mitigation of Dose-Influenced Variation in CT Quantitative Measures Using Bilateral Filtering Denoising. 2018 AAPM Annual Meeting, Nashville, TN. (August, 2018).
• Emaminejad, N., Hoffman, J., Wahi-Anwar, M., Kim, G.H., Brown, M., McNitt-Gray, M. Robustness of Lung Nodule Classification by Radiomic Texture Feature Across CT Acquisition and Reconstruction Parameters. 2018 AAPM Annual Meeting, Nashville, TN. (August, 2018).
• Wang, X., Chou, C., Hoffman, J., Emaminejad, N., Wahi-Anwar, M., McNitt-Gray, M., Brown, M. Robustness of Lung Segmentation On Ultra-Low-Dose Chest CT Using Convolutional Neural Network. 2018 AAPM Annual Meeting, Nashville, TN. (August, 2018).
• (slides) Hoffman, J., Hsieh, S., Noo, F., McNitt-Gray, M. FreeCT ICD: Free, Open-Source MBIR Reconstruction Software for Diagnostic CT. The Fifth International Conference on Image Formation in X-Ray Computed Tomography, May 20-23, 2018. Salt Lake City UT.
• Wahi-Anwar, M., Emaminejad, N., Hoffman, J., Kim, GH., Brown, M., McNitt-Gray, M. Towards quantitative imaging: stability of fully automated nodule segmentation across varied dose levels and reconstruction parameters in a low-dose CT screening patient cohort. Proc. SPIE 10575, Medical Imaging 2018: Computer-Aided Diagnosis, 105751L (27 February 2018).
• Emaminejad, N., Wahi-Anwar, M., Hoffman, J., Kim, GH., Brown, M., McNitt-Gray, M. The effects of variations in parameters and algorithm choices on calculated radiomics feature values: initial investigations and comparisons to feature variability across CT image acquisition conditions, Proc. SPIE 10575, Medical Imaging 2018: Computer-Aided Diagnosis, 105753W (2 March 2018)
• Hoffman, J., Kim, G., Goldin, J., Brown, M., McNitt-Gray, M. Robustness Evaluation of RA-950 Scoring in a Cohort of CT Lung Screening Patients Across a Large Range of CT Acquisition and Reconstruction Conditions. Radiological Society of North America 2017 Scientific Assembly and Annual Meeting, November 26 - December 1, 2017, Chicago IL.
• Emaminejad, N., Wahi-Anwar, W., Hoffman, J., Ruchalski, K., Goldin, J., Sultan, A., Kim, G., Brown M., McNitt-Gray, M. Assessing the Performance of CAD in Lung Nodule Detection from Low-Dose Lung Cancer Screening CT Exams Under Different Combinations of Radiation Dose Levels. Radiological Society of North America 2017 Scientific Assembly and Annual Meeting, November 26 - December 1, 2017, Chicago IL.
• (slides) Hoffman, J., Kim G., Goldin, J., Brown, M., McNitt-Gray, M. A Pilot Study Evaluating the Robustness of Density Mask Scoring (RA-950), a Quantitative Measure of Chronic Obstructive Pulmonary Disease, to CT Parameter Selection Using a High-Throughput, Automated, Computational Research Pipeline. American Association of Physicists in Medicine 2017. Annual Meeting and Exhibition, July 30-August 3, 2017, Denver CO.
• (poster) Hoffman, J., Wahi-Anwar W., Emaminejad N., Kim, G., Brown, M., McNitt-Gray, M. A Fully-Automated, High-Throughput, Reconstruction and Analysis Pipeline for Quantitative Imaging in CT. American Association of Physicists in Medicine 2017. Annual Meeting and Exhibition, July 30-August 3, 2017, Denver CO.
• (slides) Hoffman, J., Noo, F., McNitt-Gray, M. Influence of Tube Current Modulation on Noise Statistics of Reconstructed Images in Low-Dose Lung Cancer CT Screening. American Association of Physicists in Medicine 2017. Annual Meeting and Exhibition, July 30-August 3, 2017, Denver CO.
• Zhao, T., Hoffman, J., McNitt-Gray, M., Ruan, D. Low-Dose CT Image Denoising Using an Optimized Wiener Filter in the BM3D Algorithm. American Association of Physicists in Medicine 2017. Annual Meeting and Exhibition, July 30-August 3, 2017, Denver CO.
• Young, S., Lo, P., Hoffman, J., Kim, G., Hsu, W., Flores, C., Lee, G., Brown, M., McNitt-Gray, M. CAD Performance on a Large Cohort of National Lung Screening Trial Patients at Screening and Sub-Screening Doses. Radiological Society of North America 2016 Scientific Assembly and Annual Meeting, November 27 - December 2, 2016, Chicago IL.
• Young, S., Lo, P., Kim, G., Hsu, W., Hoffman, J., Brown, M., McNitt-Gray, M. The Effects of Reduced-Dose Lung Cancer Screening CT on Lung Nodule Detection Using a CAD Algorithm. American Association of Physicists in Medicine 2016. Annual Meeting and Exhibition, July 31-August 4, 2016, Washington, DC.
• Young, S., Hoffman, J., Noo, F., McNitt-Gray, M. Vendor-Independent, Model-Based Iterative Reconstruction on a Rotating Grid with Coordinate-Descent Optimization for CT Imaging Investigations. American Association of Physicists in Medicine 2016. Annual Meeting and Exhibition, July 31-August 4, 2016, Washington, DC.
• Lo, P., Young, S., Hoffman, J., Wahi-Anwar, W., Kim, G., McNitt-Gray, M. Effects of Dose Reduction on Emphysema Score. American Association of Physicists in Medicine 2016. Annual Meeting and Exhibition, July 31-August 4, 2016, Washington, DC.
• Young, S., Lo, P., Hoffman, J., Wahi-Anwar, W., Noo, F., Brown, M., McNitt-Gray, M., A Fully-Automated Pipeline for Generating CT Images Across a Range of Doses and Reconstruction Methods. American Association of Physicists in Medicine 2016. Annual Meeting and Exhibition, July 31-August 4, 2016, Washington, DC.
• Young, S., Lo, P., Hoffman, J., Kim, G., Hsu, W., Flores, C., Lee, G., Brown, M., McNitt-Gray, M. CT Lung Cancer Screening and the Effects of Further Dose Reduction on CAD Performance. American Association of Physicists in Medicine 2016. Annual Meeting and Exhibition, July 31-August 4, 2016, Washington, DC.
• (slides) Hoffman, J., Noo, F., Young, S., McNitt-Gray, M. Tailoring TCM Schemes to a Task: Evaluating the Impact of Customized TCM Profiles on Detection of Lung Nodules in Simulated CT Lung Cancer Screening. American Association of Physicists in Medicine 2016. Annual Meeting and Exhibition, July 31-August 4, 2016, Washington, DC.
• (slides) Hoffman, J., Noo, F., McMillan, K., Young, S., & McNitt-Gray, M. Assessing Nodule Detection on Lung Cancer Screening CT: The Effects of Tube Current Modulation and Model Observer Selection on Detectability Maps. SPIE 2016. SPIE Medical Imaging Conference, February 27-March 3, 2016, San Diego CA.
• Young, S., Lo, P., Hoffman, J., M., Kim, H. J. G., Brown, M. S., & McNitt-Gray, M. Effects of CT Dose and Nodule Characteristics on Lung-Nodule Detectability in a Cohort of 90 National Lung Screening Trial Patients. SPIE 2016. SPIE Medical Imaging Conference, February 27-March 3, 2016, San Diego CA.
• (slides) Hoffman, J., McNitt-Gray, M. A Method for Cross-platform Comparison of Reconstruction Kernels in CT. Radiological Society of North America 2015 Scientific Assembly and Annual Meeting, November 29 - December 4, 2015, Chicago IL.
• Martin, T., Hoffman, J., McNitt-Gray, M., Wang, D. Low Dose CT Perfusion Using Projection View-Sharing. Radiological Society of North America 2015 Scientific Assembly and Annual Meeting, November 29 - December 4, 2015, Chicago IL.
• (Poster) Young, S., Hoffman, J., Noo, F., McNitt-Gray, M. Development of Stand-Alone Filtered Backprojection and Iterative Reconstruction Methods Using the Raw CT Data Exported from Clinical Lung Screening Scans. American Association of Physicists in Medicine 2015. Annual Meeting and Exhibition, July 12-July 16, 2015, Anaheim CA.
• (poster) Hoffman, J., Martin, T., Young, S., McNitt-Gray, M., Wang, D. A KWIC and Dirty Look at Dose Savings and Perfusion Metrics in Simulated CT Neuro Perfusion Exams. American Association of Physicists in Medicine 2015. Annual Meeting and Exhibition, July 12-July 16, 2015, Anaheim CA.
• Lo, P., Young, S., Kim, G., Hoffman, J., Brown, M., McNitt-Gray, M. The Effects of CT Acquisition and Reconstruction Conditions on Computed Texture Feature Values of Lung Lesions. American Association of Physicists in Medicine 2015. Annual Meeting and Exhibition, July 12-July 16, 2015, Anaheim CA.
• Young, S., Lo, P., Kim, G., Hoffman, J., Brown, M., McNitt-Gray, M. A Research Pipeline to Simulate a Wide Range of CT Image Acquisition and Reconstruction Parameters and Assess the Performance of Quantitative Imaging and CAD Systems. American Association of Physicists in Medicine 2015. Annual Meeting and Exhibition, July 12-July 16, 2015, Anaheim CA.