Dan

Daniel Adler

Research Overview

I am a Ph.D. graduate from the HHMI/NIBIB Interfaces Program at the University of Pennsylvania. I conducted research under the supervision of Prof. Paul Yushkevich. Prior to working at PICSL, I completed the Perelman School of Medicine’s 1.5-year pre-clinical curriculum. A major goal of my work was to improve our understanding of hippocampal anatomy using MRI and histological imaging, towards the goal of developing improved subfield-specific biomarkers for diagnosis and treatment effect monitoring in dementia.

Postmortem atlas of the human hippocampal formation

  • We constructed a probabilistic atlas of the human hippocampal formation from fused histology and high-resolution, ex vivo MRI acquired at 9.4T from 25 specimens
  • Data for this atlas was reconstructed and co-registered with the help of HistoloZee, software that we developed for 3D reconstruction and registration of very large histology datasets. HistoloZee allows interactive co-registration of histology slides to each other and with MRI volumes. HistoloZee It also permits multi-scale viewing and management of large slide collections and it includes GPU-accelerated processing features to guide registration in real-time.

GPU-accelerated medical image registration

My M.Sc. thesis research was on leveraging the programmable GPU graphics pipeline for 3D affine and deformable medical image registration (joint work with Sonny Chan under the supervision of J. Ross Mitchell). Click here for a video of Dr. Mitchell running a demo of our software (recorded in 2007) and motivating the use of accelerated registration in the clinical setting.

Education

  • Ph.D. in Bioengineering, University of Pennsylvania, 2016
  • M.Sc. in Electrical Engineering, University of Calgary, 2010
  • B.Sc. in Computer Science and Applied Mathematics, University of Calgary, 2006

Recent journal and conference publications

  • [DOI] D. H. Adler, J. Pluta, S. Kadivar, C. Craige, J. C. Gee, B. B. Avants, and P. Yushkevich, “Histology-derived volumetric annotation of the human hippocampal subfields in postmortem MRI,” Neuroimage, vol. 84, iss. 1, pp. 505-523, 2014.
    [Bibtex]
    @ARTICLE{Adler2014N,
    author = {Adler, Daniel H. and Pluta, John and Kadivar, Salmon and Craige,
    Caryne and Gee, James C. and Avants, Brian B. and Yushkevich, Paul
    A.},
    title = {{H}istology-derived volumetric annotation of the human hippocampal
    subfields in postmortem {MRI}},
    journal = {{N}euroimage},
    year = {2014},
    volume = {84},
    pages = {505--523},
    number = {1},
    month = {Jan},
    doi = {http://dx.doi.org/10.1016/j.neuroimage.2013.08.067}
    }
  • M. Kumar, J. T. Duda, R. Ittyerah, D. Adler, S. Pickup, E. S. Brodkin, T. Abel, J. C. Gee, and H. Poptani, “High resolution diffusion tensor imaging to assess brain microstructural abnormalities in a Neuroligin-3 knockin mouse model associated with Autism spectrum disorders,” in Proceedings 21st Scientific Meeting, International Society for Magnetic Resonance in Medicine, Salt Lake City, 2013, p. 1046.
    [Bibtex]
    @INPROCEEDINGS{Kumar2013ISMRM,
    author = {Kumar, M. and Duda, J. T. and Ittyerah, R. and Adler, D. and Pickup,
    S. and Brodkin, E. S. and Abel, T. and Gee, J. C. and Poptani, H.},
    title = {{H}igh resolution diffusion tensor imaging to assess brain microstructural
    abnormalities in a {Neuroligin-3} knockin mouse model associated
    with {A}utism spectrum disorders},
    booktitle = {{P}roceedings 21st {S}cientific {M}eeting, {I}nternational {S}ociety
    for {M}agnetic {R}esonance in {M}edicine, {S}alt {L}ake {C}ity},
    year = {2013},
    pages = {1046}
    }
  • D. H. Adler, S. Chan, and J. R. Mitchell, “Affine Medical Image Registration Using the Graphics Processing Unit.” CRC Press, 2013, pp. 223-246.
    [Bibtex]
    @INBOOK{Adler2013IPRT,
    chapter = {16 of Image Processing in Radiation Therapy},
    pages = {223--246},
    title = {{A}ffine {M}edical {I}mage {R}egistration {U}sing the {G}raphics
    {P}rocessing {U}nit},
    publisher = {CRC Press},
    year = {2013},
    author = {Adler, D. H. and Chan, S. and Mitchell, J. R.}
    }
  • D. Adler, S. Kadivar, J. Pluta, S. Orozco, and P. Yushkevich, “High-resolution atlas of the human hippocampus from postmortem 9.4T MRI and reconstructed histology,” in 18th annual meeting for the Organization of Human Brain Mapping, 2012.
    [Bibtex]
    @INPROCEEDINGS{Adler2012HBM,
    author = {Adler, D. and Kadivar, S. and Pluta, J. and Orozco, S. and Yushkevich,
    P.},
    title = {{H}igh-resolution atlas of the human hippocampus from postmortem
    {9.4T MRI} and reconstructed histology},
    booktitle = {18th annual meeting for the {O}rganization of {H}uman {B}rain {M}apping},
    year = {2012}
    }
  • R. Crescenzi, D. Adler, P. A. Yushkevich, V. M. -Y. Lee, J. A. Detre, and A. Borthakur, “Early diffusion changes in a mouse model of neurofibrillary tangles,” in Proceedings 21st Scientific Meeting, International Society for Magnetic Resonance in Medicine, Melbourne, 2012, p. 975.
    [Bibtex]
    @INPROCEEDINGS{Crescenzi2012ISMRM,
    author = {Crescenzi, R. and Adler, D. and Yushkevich, P. A. and Lee, V. M.-Y.
    and Detre, J. A. and Borthakur, A.},
    title = {{E}arly diffusion changes in a mouse model of neurofibrillary tangles},
    booktitle = {{P}roceedings 21st {S}cientific {M}eeting, {I}nternational {S}ociety
    for {M}agnetic {R}esonance in {M}edicine, {M}elbourne},
    year = {2012},
    pages = {975}
    }
  • D. H. Adler, A. Y. Liu, J. Pluta, S. Kadivar, S. Orozco, H. Wang, J. C. Gee, B. B. Avants, and P. A. Yushkevich, “Reconstruction of the human hippocampus in 3D from histology and high-resolution ex-vivo MRI,” in Biomedical Imaging (ISBI), 2012 9th IEEE International Symposium on, 2012, pp. 294-297.
    [Bibtex]
    @INPROCEEDINGS{Adler2012ISBI,
    author = {Adler, Daniel H. and Liu, Alex Yang and Pluta, John and Kadivar,
    Salmon and Orozco, Sylvia and Wang, Hongzhi and Gee, James C. and
    Avants, Brian B. and Yushkevich, Paul A.},
    title = {{R}econstruction of the human hippocampus in {3D} from histology
    and high-resolution ex-vivo {MRI}},
    booktitle = {{B}iomedical {I}maging {(ISBI)}, 2012 9th {IEEE} {I}nternational
    {S}ymposium on},
    year = {2012},
    pages = {294--297}
    }
  • S. Drabycz, G. Roldán, P. de Robles, D. Adler, J. B. McIntyre, A. M. Magliocco, J. G. Cairncross, and J. R. Mitchell, “Analysis of MGMT promoter methylation status in high grade glioma patients with long term and conventional survival times: a retrospective study,” Neuroimage, vol. 49, iss. 2, 2010.
    [Bibtex]
    @ARTICLE{Drabycz2010N,
    author = {Drabycz, S. and Rold\'an, G. and de Robles, P. and Adler, D. and
    McIntyre, J. B. and Magliocco, A. M. and Cairncross, J. G. and Mitchell,
    J. R.},
    title = {{A}nalysis of {MGMT} promoter methylation status in high grade glioma
    patients with long term and conventional survival times: a retrospective
    study},
    journal = {{N}euroimage},
    year = {2010},
    volume = {49},
    number = {2},
    page = {1398--1405}
    }
  • T. A. Bjarnason, S. Drabycz, D. H. Adler, J. G. Cairncross, and J. R. Mitchell, “Applying the S-transform to magnetic resonance imaging texture analysis,” Fields Institute Communications, vol. 52, 2007.
    [Bibtex]
    @ARTICLE{Bjarnason2007fields,
    author = {Bjarnason, T. A. and Drabycz, S. and Adler, D. H. and Cairncross,
    J. G. and Mitchell, J. R.},
    title = {{A}pplying the {S}-transform to magnetic resonance imaging texture
    analysis},
    journal = {{F}ields {I}nstitute {C}ommunications},
    year = {2007},
    volume = {52},
    page = {311--321}
    }
  • W. F. Teskey, D. H. Adler, and W. J. Teskey, “Determining free flight performance by surveying engineering techniques,” J Surv Eng, vol. 132, iss. 2, 2006.
    [Bibtex]
    @ARTICLE{Teskey2006jsengg,
    author = {Teskey, W. F. and Adler, D. H. and Teskey, W. J.},
    title = {{D}etermining free flight performance by surveying engineering techniques},
    journal = {{J} {S}urv {E}ng},
    year = {2006},
    volume = {132},
    number = {2},
    page = {93--96}
    }
  • M. Oleson, D. Adler, and P. Goldsmith, “A comparison of forefoot stiffness in running and running shoe bending stiffness,” J Biomech, vol. 38, iss. 9, 2005.
    [Bibtex]
    @ARTICLE{Oleson2005jbiomech,
    author = {Oleson, M. and Adler, D. and Goldsmith, P.},
    title = {{A} comparison of forefoot stiffness in running and running shoe
    bending stiffness},
    journal = {{J} {B}iomech},
    year = {2005},
    volume = {38},
    number = {9},
    page = {1886--1894}
    }
  • W. F. Teskey, R. J. Fox, and D. H. Adler, “Hidden Point Bar method for precise heighting,” J Surv Eng, vol. 130, iss. 4, 2004.
    [Bibtex]
    @ARTICLE{Teskey2004jsengg,
    author = {Teskey, W. F. and Fox, R. J. and Adler, D. H.},
    title = {{H}idden {P}oint {B}ar method for precise heighting},
    journal = {{J} {S}urv {E}ng},
    year = {2004},
    volume = {130},
    number = {4},
    page = {179--182}
    }