Jason Crane, PhD
Director, Computational Core
Radiology
School of Medicine

Education & Training

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• B.A. Chemistry Brandeis University
• PhD Physical Chemistry University of California, Berkeley
• MS Physical Chemistry University of Chicago
• Postdoc Physical Chemistry University of Illinois

Interests

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• product development
• data science
• Open Source Software
• machine learning
• Scientific Software
• Cloud Computing
• Medical Imaging
• Translational Research
• Spectroscopy
• informatics
• computational health
• High Performance Computing

Websites

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• UCSF Bridge (bridge.ucsf.edu)
• UCSF Information Commons (informationcommons.ucsf.edu)
• Center For Intelligent Imaging (intelligentimaging.ucsf.edu)
• SIVIC Software Project (sourceforge.net)
• SIVIC Github (github.com)

Publications (49)

Top publication keywords:
RadiologistsEcho-Planar ImagingOligodendrogliomaBrainGlioblastomaGliomaMagnetic Resonance SpectroscopyCarbon IsotopesPyruvic AcidBrain NeoplasmsMagnetic Resonance ImagingMachine LearningProstateIsocitrate DehydrogenaseSignal-To-Noise Ratio

• Data Format Standardization and DICOM Integration for Hyperpolarized 13C MRI.
  ArXiv 2024 Diaz E, Sriram R, Gordon JW, Sinha A, Liu X, Sahin S, Crane J, Olson MP, Chen HY, Bernard J, Vigneron DB, Wang ZJ, Xu D, Larson PEZ
• Data Format Standardization and DICOM Integration for Hyperpolarized 13C MRI.
  Journal of imaging informatics in medicine 2024 Diaz E, Sriram R, Gordon JW, Sinha A, Liu X, Sahin SI, Crane JC, Olson MP, Chen HY, Bernard JML, Vigneron DB, Wang ZJ, Xu D, Larson PEZ
• NIMG-25. CLINICAL FEASIBILITY OF AI-BASED T2 FLAIR SEGMENTATION FOR DETECTION OF PROGRESSION IN NON-ENHANCING LOWER GRADE GLIOMA.
  Neuro-Oncology 2023 Tracy Luks, Pablo Damasceno, Tyler Gleason, James Hawkins, Lauro Avalos, Shawn Hervey-Jumper, Sharmila Majumdar, Janine Lupo, Jason Crane, Javier Villanueva-Meyer
• Implementation and prospective real-time evaluation of a generalized system for in-clinic deployment and validation of machine learning models in radiology.
  PLOS digital health 2023 Hawkins JR, Olson MP, Harouni A, Qin MM, Hess CP, Majumdar S, Crane JC
• Interactive Effects of Molecular, Therapeutic, and Patient Factors on Outcome of Diffuse Low-Grade Glioma.
  Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2023 Hervey-Jumper SL, Zhang Y, Phillips JJ, Morshed RA, Young JS, McCoy L, Lafontaine M, Luks T, Ammanuel S, Kakaizada S, Egladyous A, Gogos A, Villanueva-Meyer J, Shai A, Warrier G, Rice T, Crane J, …

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• Utilizing a Digital Swarm Intelligence Platform to Improve Consensus Among Radiologists and Exploring Its Applications.
  Journal of digital imaging 2022 Shah R, Astuto Arouche Nunes B, Gleason T, Fletcher W, Banaga J, Sweetwood K, Ye A, Patel R, McGill K, Link T, Crane J, Pedoia V, Majumdar S
• Improving the Automatic Classification of Brain MRI Acquisition Contrast with Machine Learning.
  Journal of digital imaging 2022 Cluceru J, Lupo JM, Interian Y, Bove R, Crane JC
• Federated learning for predicting clinical outcomes in patients with COVID-19.
  Nature medicine 2021 Dayan I, Roth HR, Zhong A, Harouni A, Gentili A, Abidin AZ, Liu A, Costa AB, Wood BJ, Tsai CS, Wang CH, Hsu CN, Lee CK, Ruan P, Xu D, Wu D, Huang E, Kitamura FC, Lacey G, de Antônio Corradi GC, Nino G…
• Federated Learning used for predicting outcomes in SARS-COV-2 patients.
  Research square 2021 Flores M, Dayan I, Roth H, Zhong A, Harouni A, Gentili A, Abidin A, Liu A, Costa A, Wood B, Tsai CS, Wang CH, Hsu CN, Lee CK, Ruan C, Xu D, Wu D, Huang E, Kitamura F, Lacey G, César de Antônio Corradi…
• NIMG-44. INTEGRATING AUTOMATED LESION SEGMENTATIONS FROM SINGLE-IMAGES INTO ROUTINE CLINICAL WORKFLOW FOR VOLUMETRIC RESPONSE ASSESSMENT.
  Neuro-Oncology 2020 Javier Villanueva-Meyer, Pablo Damasceno, Marisa LaFontaine, James Hawkins, Tracy Luks, Jason Crane, Janine Lupo
• SURG-18. THE IMPACT OF NEUROLOGIC IMPAIRMENTS ON THE RELATIVE BENEFIT OF MAXIMAL EXTENT OF RESECTION IN NEWLY DIAGNOSED IDH-WILD TYPE GLIOBLASTOMA.
  Neuro-Oncology 2020 Shawn Hervey-Jumper, Annette Molinaro, Cecilia Dalle Ore, Desmond Brown, Yalan Zhang, Ramin Morshed, Marisa LaFontaine, Simon Ammanuel, Anny Shai, Gayathri Warrier, Terri Rice, Yi Lin, Jason Crane, …
• Association of Maximal Extent of Resection of Contrast-Enhanced and Non-Contrast-Enhanced Tumor With Survival Within Molecular Subgroups of Patients With Newly Diagnosed Glioblastoma.
  JAMA oncology 2020 Molinaro AM, Hervey-Jumper S, Morshed RA, Young J, Han SJ, Chunduru P, Zhang Y, Phillips JJ, Shai A, Lafontaine M, Crane J, Chandra A, Flanigan P, Jahangiri A, Cioffi G, Ostrom Q, Anderson JE, Badve C…
• Hyperpolarized 13 C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco.
  NMR in biomedicine 2020 Crane JC, Gordon JW, Chen HY, Autry AW, Li Y, Olson MP, Kurhanewicz J, Vigneron DB, Larson PEZ, Xu D
• Kinetic Modeling of Hyperpolarized Carbon-13 Pyruvate Metabolism in the Human Brain.
  IEEE transactions on medical imaging 2019 Mammoli D, Gordon J, Autry A, Larson PEZ, Li Y, Chen HY, Chung B, Shin P, Van Criekinge M, Carvajal L, Slater JB, Bok R, Crane J, Xu D, Chang S, Vigneron DB
• NIMG-66. COMPARISON OF STEADY STATE AND DYNAMIC BRAIN METABOLISM BY USING 1H MRSI AND HYPERPOLARIZED [1-13C]PYRUVATE IMAGING IN PATIENTS WITH GLIOMA.
  Neuro-Oncology 2018 Yan Li, Adam Autry, Jeremy Gordon, Jason Crane, Beck Olson, Marisa Lafontaine, Ilwoo Park, Javier Villanueva-Meyer, Daniel Vigneron, Susan Chang, Sarah Nelson
• Reliable and Reproducible GABA Measurements Using Automated Spectral Prescription at Ultra-High Field.
  Frontiers in human neuroscience 2017 Li Y, Bian W, Larson P, Crane JC, Parvathaneni P, Nagarajan S, Nelson SJ
• Automated Prescription and Reconstruction of Brain MR Spectroscopy Data for Rapid Integration into the Clinical Workflow
  Neurological Disorders & Epilepsy Journal 2017 Jason C. Crane, Yan Li, Marram P. Olson, Marisa Lafontaine, Stojan Maleschlijski, Wei Bian, Christopher P. Hess and Sarah J. Nelson
• Fully automated atlas-based method for prescribing 3D PRESS MR spectroscopic imaging: Toward robust and reproducible metabolite measurements in human brain.
  Magnetic resonance in medicine 2017 Bian W, Li Y, Crane JC, Nelson SJ
• Metabolic Profiling of IDH Mutation and Malignant Progression in Infiltrating Glioma.
  Scientific reports 2017 Jalbert LE, Elkhaled A, Phillips JJ, Neill E, Williams A, Crane JC, Olson MP, Molinaro AM, Berger MS, Kurhanewicz J, Ronen SM, Chang SM, Nelson SJ
• Association of early changes in 1H MRSI parameters with survival for patients with newly diagnosed glioblastoma receiving a multimodality treatment regimen.
  Neuro-oncology 2017 Nelson SJ, Kadambi AK, Park I, Li Y, Crane J, Olson M, Molinaro A, Roy R, Butowski N, Cha S, Chang S
• NIMG-32. 3D SHORT AND LONG ECHO TIME 1H MRSI IN PATIENTS WITH NON-ENHANCING GLIOMAS.
  Neuro-Oncology 2016 Yan Li, Tracy Luks, Jason Crane, Sarah Nelson, Tracy McKnight
• Serial analysis of 3D H-1 MRSI for patients with newly diagnosed GBM treated with combination therapy that includes bevacizumab.
  Journal of neuro-oncology 2016 Nelson SJ, Li Y, Lupo JM, Olson M, Crane JC, Molinaro A, Roy R, Clarke J, Butowski N, Prados M, Cha S, Chang SM
• Detection of localized changes in the metabolism of hyperpolarized gluconeogenic precursors 13 C-lactate and 13 C-pyruvate in kidney and liver.
  Magnetic resonance in medicine 2016 von Morze C, Chang GY, Larson PE, Shang H, Allu PK, Bok RA, Crane JC, Olson MP, Tan CT, Marco-Rius I, Nelson SJ, Kurhanewicz J, Pearce D, Vigneron DB
• Detecting Metabolism of Gluconeogenic Precursors Lactate and Pyruvate in Kidney & Liver with Hyperpolarized 13 C MRI.
  The FASEB Journal 2016 Cornelius von Morze, Gene-Yuan Chang, Peder E Larson, Hong Shang, Prasanna KR Allu, Robert A Bok, Jason C Crane, Marram P Olson, Chou T Tan, Irene Marco-Rius, Sarah J Nelson, John Kurhanewicz, David …
• Power estimation for non-standardized multisite studies.
  NeuroImage 2016 Keshavan A, Paul F, Beyer MK, Zhu AH, Papinutto N, Shinohara RT, Stern W, Amann M, Bakshi R, Bischof A, Carriero A, Comabella M, Crane JC, D'Alfonso S, Demaerel P, Dubois B, Filippi M, Fleischer V, …
• NI-79RAPID ASSESSMENT OF LESION VOLUMES FOR PATIENTS WITH GLIOMA USING THE SMARTBRUSH SOFTWARE PACKAGE.
  Neuro-Oncology 2014 Sana Vaziri, Marisa Lafontaine, Beck Olson, Jason C. Crane, Susan Chang, Janine Lupo, Sarah J. Nelson
• Precision medicine in chronic disease management: The multiple sclerosis BioScreen.
  Annals of neurology 2014 Gourraud PA, Henry RG, Cree BA, Crane JC, Lizee A, Olson MP, Santaniello AV, Datta E, Zhu AH, Bevan CJ, Gelfand JM, Graves JS, Goodin DS, Green AJ, von Büdingen HC, Waubant E, Zamvil SS, Crabtree-…
• SIVIC: Open-Source, Standards-Based Software for DICOM MR Spectroscopy Workflows.
  International journal of biomedical imaging 2013 Crane JC, Olson MP, Nelson SJ
• Imaging biomarkers of ramucirumab and olaratumab in patients with recurrent glioblastoma.
  Journal of Clinical Oncology 2013 Jaishri O'Neill Blakeley, Joy D. Fisher, Frank S. Lieberman, Janine Lupo, Louis B. Nabors, Jason Crane, Patrick Y. Wen, Andre Cote, David M. Peereboom, Qiuting Wen, Timothy Francis Cloughesy, H. Ian …
• Strategies for rapid in vivo 1H and hyperpolarized 13C MR spectroscopic imaging.
  Journal of magnetic resonance (San Diego, Calif. : 1997) 2013 Nelson SJ, Ozhinsky E, Li Y, Park Iw, Crane J
• Prospective image registration for automated scan prescription of follow-up knee images in quantitative studies.
  Magnetic resonance imaging 2011 Goldenstein J, Schooler J, Crane JC, Ozhinsky E, Pialat JB, Carballido-Gamio J, Majumdar S
• Serial analysis of imaging parameters in patients with newly diagnosed glioblastoma multiforme.
  Neuro-oncology 2011 Li Y, Lupo JM, Polley MY, Crane JC, Bian W, Cha S, Chang S, Nelson SJ
• 3D sensitivity encoded ellipsoidal MR spectroscopic imaging of gliomas at 3T.
  Magnetic resonance imaging 2009 Ozturk-Isik E, Chen AP, Crane JC, Bian W, Xu D, Han ET, Chang SM, Vigneron DB, Nelson SJ
• A clinical comparison of rigid and inflatable endorectal-coil probes for MRI and 3D MR spectroscopic imaging (MRSI) of the prostate.
  Journal of magnetic resonance imaging : JMRI 2008 Noworolski SM, Crane JC, Vigneron DB, Kurhanewicz J
• Compressed sensing for resolution enhancement of hyperpolarized 13C flyback 3D-MRSI.
  Journal of magnetic resonance (San Diego, Calif. : 1997) 2008 Hu S, Lustig M, Chen AP, Crane J, Kerr A, Kelley DA, Hurd R, Kurhanewicz J, Nelson SJ, Pauly JM, Vigneron DB
• Three-dimensional J-resolved H-1 magnetic resonance spectroscopic imaging of volunteers and patients with brain tumors at 3T.
  Magnetic resonance in medicine 2007 Li Y, Chen AP, Crane JC, Chang SM, Vigneron DB, Nelson SJ
• Grid enabled magnetic resonance scanners for near real-time medical image processing
  Journal of Parallel and Distributed Computing 2006 Crane JC, Crawford FW, Nelson SJ
• Grid enabled magnetic resonance scanners for near real-time medical image processing.
  Journal of Parallel and Distributed Computing 2006 Jason C. Crane, Forrest W. Crawford, Sarah J. Nelson
• Considerations in applying 3D PRESS H-1 brain MRSI with an eight-channel phased-array coil at 3 T.
  Magnetic resonance imaging 2006 Li Y, Osorio JA, Ozturk-Isik E, Chen AP, Xu D, Crane JC, Cha S, Chang S, Berger MS, Vigneron DB, Nelson SJ
• A feasibility study of in vivo T1rho imaging of the intervertebral disc.
  Magnetic resonance imaging 2006 Blumenkrantz G, Li X, Han ET, Newitt DC, Crane JC, Link TM, Majumdar S
• Unaliasing lipid contamination for MR spectroscopic imaging of gliomas at 3T using sensitivity encoding (SENSE).
  Magnetic resonance in medicine 2006 Ozturk-Isik E, Crane JC, Cha S, Chang SM, Berger MS, Nelson SJ
• Quantitative apparent diffusion coefficients and T2 relaxation times in characterizing contrast enhancing brain tumors and regions of peritumoral edema.
  Journal of magnetic resonance imaging : JMRI 2005 Oh J, Cha S, Aiken AH, Han ET, Crane JC, Stainsby JA, Wright GA, Dillon WP, Nelson SJ
• The folding mechanism of a beta-sheet: the WW domain.
  Journal of molecular biology 2001 Jäger M, Nguyen H, Crane JC, Kelly JW, Gruebele M
• Mapping the transition state of the WW domain beta-sheet.
  Journal of molecular biology 2000 Crane JC, Koepf EK, Kelly JW, Gruebele M
• Stimulated Emission Pumping Spectra and Intramolecular Vibrational Dynamics of DFCO(S 0 ) from 9000 to 20 000 cm -1.
  The Journal of Physical Chemistry A 1998 Jason C. Crane, Hakhyun Nam, Horst Clauberg, Harry P. Beal, Ilia J. Kalinovski, Richard G. Shu, C. Bradley Moore
• Stimulated emission pumping spectra and intramolecular vibrational dynamics of DFCO(S0) from 9000 to 20,000 cm(-1)
  The journal of physical chemistry. A 1998 Crane JC, Nam H, Clauberg H, Beal HP, Kalinovski IJ, Shu RG, Moore CB
• Vibrational Assignment and Anharmonic Resonance Analysis of the Dispersed Fluorescence and Stimulated Emission Pumping Spectra of DFCO (S 0 ) up to 9000 cm-1
  Journal of Molecular Spectroscopy 1997 Crane JC, Kawai A , Nam H , Clauberg H , Beal HP , Guinn P , Moore CB
• Vibrational Assignment of theS1Fluorescence Excitation Spectrum of Formyl Fluoride.
  Journal of Molecular Spectroscopy 1997 Jason C. Crane, Hakhyun Nam, Harry P. Beal, Horst Clauberg, Young S. Choi, C.Bradley Moore, John F. Stanton
• Vibrational Assignment of theS1Fluorescence Excitation Spectrum of Formyl Fluoride
  Journal of Molecular Spectroscopy 1996 Crane JC, Hakhyun Nam, Harry P. Beal, Horst Clauberg, Young S. Choi, C.Bradley Moore, John F. Stanton