Publications

2017

BIM-Sim: Interactive Simulation of Broadband Imaging Using Mie Theory
Sebastian Berisha, Thomas van Dijk, Rohit Bhargava, P. Scott Carney, and David Mayerich
Frontiers in Physics, 5:5, February 2017
[Paper]

SIproc: an open-source biomedical data processing platform for large hyperspectral images
Sebastian Berisha, Shengyuan Chang, Sam Saki, Davar Daeinejad, Ziqi He, Rupali Mankar, and David Mayerich
Analyst, 142(8): 1350-1357, April 2017
[Paper]

Image-Guided, Laser-Based Fabrication of Vascular-Derived Microfluidic Networks
Keely Heintz, David Mayerich, and John Slater
Journal of Visualized Experiments, (119): e55101, January 2017
[Paper]

2016

Multimodal embryonic imaging using optical coherence tomography, selective plane illumination microscopy, and optical projection tomography
Manmohan Singh, Chen Wu, David Mayerich, Mary Dickinson, Irina Larina, and Kirill Larin
IEEE Engineering in Medicine and Biology Society (EMBC), August 2016
[Paper]

Comparison of rotational imaging optical coherence tomography and selective plane illumination microscopy for embryonic study
Chen Wu, Shihao Ran, Henry Le, Manmohan Singh, Irina Larina, David Mayerich, Mary Dickinson, Kirill Larin
Proceedings SPIE, Optical Methods in Developmental Biology IV, March 2016
[Paper]

2015

High definition infrared spectroscopic imaging for lymph node histopathology
L. Suzanne Leslie, Tomasz P. Wrobel, David Mayerich, Snehal Bindra, Rajyasree Emmadi, and Rohit Bhargava
PLoS One, 10(6): e0127238, 2015
[Paper]

Compositional prior information in computed infrared spectroscopic imaging
Bradley Deutsch, Rohith Reddy, David Mayerich, Rohit Bhargava, and P. Scott Carney.
Journal of the Optical Society of America (JOSA) A, 32(6):1126-1131, May 2015
[Paper]

Stain-less staining for computed histopathology
David Mayerich, Michael Walsh, Andre Kadjacsy-Balla, Partha Ray, Stephen Hewitt, and Rohit Bhargava.
Technology, 03(1):27, March 2015
[Paper]

2014

On the importance of image formation optics in the design of infrared spectroscopic imaging systems
David Mayerich, Thomas van Dijk, Michael Walsh, Matthew Schulmerich, P. Scott Carney, Rohit Bhargava
Analyst, 139(16): 4031-4036, April 2014
[Paper]

Breast histopathology using random decision forests-based classification of infrared spectroscopic imaging data
David Mayerich, Michael Walsh, Andre Kadjacsy-Balla, Shachi Mittal, Rohit Bhargava.
Proceedings of SPIE Medical Imaging 2014: Digital Pathology, 9041(904107), May 2015
[Paper]

Previous Work

Real-Time Interactive Data Mining for Chemical Imaging Information: Application to Automated Histopathology
David Mayerich, Michael Walsh, Matthew Schulmerich, and Rohit Bhargava.
BMC Bioinformatics, 14:156, May 2013
[Paper]

Rapid Spectral-Domain Localization
Thomas van Dijk, David Mayerich, Rohit Bhargava, and P. Scott Carney.
Optics Express, 21(10):12822-12830, May 2013
(Also appears in The Virtual Journal for Biomedical Optics)
[Paper]

Using High-Performance Computing to Augment Spectroscopic Imaging Systems
David Mayerich, Thomas van Dijk, Maxim Sigalov, Edo Roth, Michael Walsh, Rohith Reddy, Brynmore Davis, P. Scott Carney, and Rohit Bhargava.
Computer Science and Engineering Annual Meeting, University of Illinois at Urbana-Champaign, Apr. 2013
(3rd Place - David Kuck Poster Competition)
[Poster]

Recovery of Absorption Spectra from Fourier Transform Infrared Microspectroscopic Measurements of Intact Spheres
Thomas van Dijk, David Mayerich, P. Scott Carney, and Rohit Bhargava.
Applied Spectroscopy, 67(5):546-552, Apr. 2013
[Paper]

Volume Visualization in Serial Electron Microscopy Using Local Variance
David Mayerich and John Hart.
IEEE Symposium on Biological Data Visualization (BioVis), pp. 9-16, Oct. 2012
[Paper]

NetMets: Software for Quantifying and Visualizing Errors in Biological Network Segmentation
David Mayerich, Chris Bjornsson, Jonathan Taylor, and Badrinath Roysam.
BMC Bioinformatics, 13(Suppl 8):S7, May 2012
[Paper]

Optimizing the Design of FT-IR Spectroscopic Imaging Instruments to Obtain Increased Spatial Resolution of Chemical Species
Rohith Reddy, David Mayerich, Michael Walsh, Matthew Schulmerich, Paul Scott Carney, Rohit Bhargava.
IEEE International Symposium on Biomedical Imaging (ISBI), pp. 354-357, May 2012
[Paper]

Rigorous Electromagnetic Model of FT-IR Spectroscopic Imaging Applied to Automated Histology of Prostate Tissue Specimens
Rohith Reddy, David Mayerich, Michael Walsh, P. Scott Carney, Rohit Bhargava.
International Conference on Optics, Lasers and Spectroscopy (ICOLS), pp. 489-493, Mar. 2012
[Paper]

Specimen Preparation, Imaging, and Analysis Protocols for Knife-Edge Scanning Microscopy
Yoonsuck Choe, David Mayerich, Jaerock Kwon, Daniel Miller, Chul Sung, Ji Ryang Chung, Todd Huffman, John Keyser, Louise Abbott.
Journal of Visualized Experiments (58), e3248, Dec. 2011
[Paper/Video]

Metrics for Comparing Explicit Representations of Interconnected Biological Networks
David Mayerich, Chris Bjornsson, Jonathan Taylor, Badrinath Roysam.
IEEE Symposium on Biological Data Visualization (BioVis), pp. 79-86, Oct. 2011
[Paper]

Designing Transfer Functions for Exploring Hyperspectral Images
David Mayerich, Michael Walsh, Rohit Bhargava,
Proceedings IEEE Visualization (IEEE Vis Posters), Oct. 2011
[Short Paper]

Fast Macro-Scale Imaging of Microvascular Networks Using Transmission KESM
David Mayerich, Jaerock Kwon, Chul Sung, Louise Abbott, John Keyser, Yoonsuck Choe.
Biomedical Optics Express, 2(10): 2888-2896, Oct. 2011
[Paper]

Multiscale Exploration of Mouse Brain Microstructures Using the Knife-Edge Scanning Microscope Brain Atlas
Ji Ryang Chung, Chul Sung, David Mayerich, Jaerock Kwon, Daniel Miller, Todd Huffman, John Keyser, Louise Abbott, Yoonsuck Choe.
Frontiers in Neuroinformatics, 5:29, Nov. 2011.
(special topic on Mapping the Connectome: Multi-Level Analysis of Brain Connectivity)
[Paper][Atlas]

Knife-Edge Scanning Microscopy for Connectomics Research
Yoonsuck Choe, David Mayerich, Jaerock Kwon, Daniel Miller, Ji Ryang Chung, Chul Sung, John Keyser, Louise Abbott.
IEEE International Joint Conference on Neural Networks (IJCNN), pp. 2258-2265, Jul. 2011
[Paper]

Comparing the MOST Technique to KESM
David Mayerich, Yoonsuck Choe, John Keyser, Jaerock Kwon, Louise Abbott.
Science E-Letters, Apr. 2011
[Letter]

Automated Cropping and Artifact Removal for Knife-Edge Scanning Microscopy
Jaerock Kwon, David Mayerich, Yoonsuck Choe.
IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pp. 1366-1369, Mar. 2011
[Paper]

GPU-based Dynamic Tubular Grids for Sparse Volume Rendering
David Mayerich, John Keyser.
Proceedings of IEEE Visualization (IEEE Vis Posters), Oct. 2010.
[Short Paper] [Poster]

Charting Out the Octopus Connectome at Submicron Resolution Using the Knife-Edge Scanning Microscope
Yoonsuck Choe, Louise Abbott, Giovanna Ponte, John Keyser, Jaerock Kwon, David Mayerich, Daniel Miller, Donghyeop Han, Anna Grimaldi, Graziano Fiorito, David Edelman, Jeffrey McKinstry.
BMC Neuroscience, Jul. 2010.
(appears in Proceedings of the 19th Annual Computational Neuroscience Meeting - CNS*2010)
[Short Paper]

Hardware Accelerated Segmentation of Complex Volumetric Filament Networks
David Mayerich, John Keyser.
IEEE Transactions on Visualization and Computer Graphics, 15(4): 670-681, Jul.-Aug. 2009.
[Paper]

Visualization of Cellular and Microvascular Relationships
David Mayerich, Louise Abbott, John Keyser.
IEEE Transactions on Visualization and Computer Graphics, 14(6): 1611-1618, Nov.-Dec. 2008.
(appears in Proceedings of IEEE Visualization 2008)
[Paper]

Knife-Edge Scanning Microscopy for Imaging and Reconstruction of Three-Dimensional Anatomical Structures of the Mouse Brain
David Mayerich, Louise Abbott, Bruce McCormick.
Journal of Microscopy, 231(1): 134-143, Jul. 2008.
(cover image)
[Paper]

Constructing High-Resolution Microvascular Models
David Mayerich, Jaerock Kwon, Yoonsuck Choe, Louise Abbott, John Keyser.
Microscopic Image Analysis with Applications in Biology (MIAAB), Sept. 2008
(images appear in Portraits of the Mind: Visualizing the Brain from Antiquity to the 21st Century, C. Schoonover - ed.)
[Paper] [Book]

Filament Tracking and Encoding for Complex Biological Networks
David Mayerich, John Keyser.
Proceedings of the ACM Symposium on Solid and Physical Modeling (SPM Poster), Jun. 2008
[Short Paper]

Automated Lateral Sectioning for Knife-Edge Scanning Microscopy
Jaerock Kwon, David Mayerich, Yoonsuck Choe, Bruce McCormick.
IEEE International Symposium on Biomedical Imaging (IEEE ISBI), May 2008
[Paper]

Noise and Artifact Removal in Knife-Edge Scanning Microscopy
David Mayerich, Bruce McCormick, John Keyser.
IEEE International Symposium on Biomedical Imaging (IEEE ISBI), Apr. 2007
[Paper]

Visualization of Fibrous and Thread-like Data
Zeki Melek, David Mayerich, Cem Yuksel, John Keyser.
IEEE Transactions on Visualization and Computer Graphics, 12(5): 1165-1172, Oct. 2006.
(appears in Proceedings of IEEE Visualization 2006)
[Paper]

Construction of Anatomically Correct Models of Mouse Brain Networks
Bruce McCormick, Wonryull Koh, Yoonsuck Choe, Louise Abbott, John Keyser, David Mayerich, Zeki Melek, Purna Doddapaneni.
Neurocomputing, 58-60: 379-386, Apr. 2004.
[Paper]