CV

Summary:

PhD in physics; specializing in nonlinear optics, spectroscopy, imaging, and computational analysis
10+ years of optics and photonics experience
10+ years of LabVIEW, MATLAB, Mathematica, and other computational experience
Quantitative image acquisition and analysis, LIDAR and DIAL systems, fluorescence microscopy, nonlinear optics, ultrafast spectroscopy, optimizing and characterizing laser systems, numerical modeling, instrument automation, liquid crystal devices, prototype development and characterization, tunable spectral filters, microscopic optical devices
I am passionate about science, laser based technology, and pushing the limits of optical technologies

Education

2016 PhD in Physics, from Montana State University

2014 M.S. in Physics, from Montana State University

2011 B.S. in Physics, Minor in Mathematics, from Montana State University

Employment History

Professional

2021-Present Director of Research and Development, Aplenglow Biosciences

2017 Research Scientist, Advanced Microcavity Sensors

Academic

2017-2021 Washington Research Foundation Postdoctoral Fellow, Gerner Lab, University of Washington (UW)

2016-2017 Research Scientist, Spectrum Lab, Montana State University (MSU)

2016 Teaching Assistant, Introductory Physics, and Advanced Optics (MSU)

2012-2016 Graduate Research Assistant, Rebane lab (MSU)

2012 Research Assistant, Repasky lab (MSU)

2010-2011 Undergraduate Research Assistant, Spectrum Lab (MSU)

2010 Teaching Assistant, Holography Lab (MSU)

Volunteer

2021-Present Washington Research Foundation Postdoctoral Fellowship Selection Committee

2004-2005 Board Member, Project Manager, and Event Coordinator, Bozeman Youth Initiative (non-profit)

Experience

Programing

MATLAB/Mathematica/Python - image analysis, numerical modeling, object oriented programing, data analysis, and machine learning

LabVIEW - instrument automation and data acquisition

Other; ImageJ/Fiji, Origin, Excel, Word, PowerPoint, Imaris, Aivia, leica LASX, FlowJo, Prism, 3D modeling software (Autodesk)

Optical Devices / Lab Skills

I have experience using HeNe, DFB, DPSS, high power lasers, pulsed, and femtosecond lasers, regenerative amplifiers (including alignment and initial setup / construction of these systems), laser cooling systems, beam splitters, mirrors, attenuators, interferometers, diffractive optical elements, monochromators, spectrometers, optical spectrum analyzers, nonlinear crystals, acousto-optic modulators, optical parametric amplifiers, optical fiber systems, ellipsometers, autocorrelators, digital multimeters, oscilloscopes, DACs, high voltage power supplies, photodetectors, CCD cameras (both cooled and room temperature), microscopes (two-photon, confocal, and other custom systems), and other devices related to assembling and characterizing optical systems.

Educational

I have excelled in courses covering many topics such as nonlinear optics, Fourier optics, statistical mechanics, classical mechanics (orbital mechanics), quantum field theory, numerical computation, mathematical methods, quantum mechanics, laser physics, advanced optics, holography, laboratory electronics, and laboratory methods.

Professional Development and Research

Select Conference Presentations

2019 Hallmarks of Cancer, Seattle WA, USA. Utilizing Machine Learning and Quantitative Imaging to Explore Tumor Microenvironments

2019 BioImage Informatics, Seattle WA, USA. Quantification and visualization of tissue microenvironments and cellular interactions by clustering neighborhoods using CytoMAP

2018 World Molecular Imaging Congress, Seattle WA, USA. Utilizing Machine Learning and Quantitative Imaging to Visualize Tissue Microenvironments

2015 HBSM, Tartu Estonia. Wide field of view, broadly wavelength-tunable two-photon imaging; principles and applications

2014 SPIE Photonics West, San Francisco CA, USA. A multidimensional screening method for the selection of two-photon fluorescent proteins

2013 SPIE Photonics West, San Francisco CA, USA. Multiphoton bleaching of red fluorescent proteins

Honors and Awards

2019-2021 Washington Research Foundation Postdoctoral Fellowship

2011 Graduated with Honors, Montana State University

2010-2011 USP Scholarship, Montana State University

Select Publications

Stoltzfus, Caleb R., Jakub Filipek, Benjamin H. Gern, Brandy E. Olin, Joseph M. Leal, Yajun Wu, Miranda R. Lyons-Cohen et al. CytoMAP: a spatial analysis toolbox reveals features of myeloid cell organization in lymphoid tissues. Cell reports 31, no. 3 107523 (2020)
C. R. Stoltzfus and A. Rebane, Optimizing ultrafast illumination for multiphoton-excited fluorescence imaging, Biomed. Opt. Express 7 , 1768-1782, (2016).
C. R. Stoltzfus, L. M. Barnett, G. Wicks, A. Mikhaylov, T. E. Hughes, and A. Rebane, Two-photon directed evolution of green fluorescent proteins, Sci. Rep. 5 , 11968 (2015).

Research

Gerner Lab

I worked on an interdisciplinary research project in Michael Gerner's lab at the University of Washington, attempting to elucidate how the spatial organization of immune cells in tumor microenvironments influence disease progression and treatment outcomes. Specifically, I used multi-dimensional spectrally resolved confocal microscopy to probe the local environments of immune cells. This research involved imaging large tissue sections and developing software tools to interrogate the cellular composition, global tissue architecture, and location and type of cell-cell interactions.

Spectrum Lab (MSU) and Advanced Microcavity Sensors

I worked on a collaborative project with Advanced Microcavity Sensors LLC and MSU. I characterized and developed a high resolution, liquid crystal, tunable micro-optical filter, as well as laser systems. These systems use microscopic concave mirrors to form an optical cavity with excellent spectral resolution. This project aimed to achieve a robust and high performance-to-cost spectral system that can be integrated into existing microscope and other imaging technologies.

Rebane Lab

In Dr. Aleksander Rebane's lab I co-invented and optimized a wide field-of-view two-photon imaging system capable of capturing the two-photon excited fluorescence of ~10 cm-sized samples. We used this new imaging system combined with automated image analysis techniques I developed to evolve the two-photon brightness of fluorescent proteins commonly used in two-photon microscopy and neurological imaging studies. These brighter fluorescent proteins improve the imaging depth possible with two-photon microscope systems. We also utilized our two-photon imaging technique to image fluorescently stained latent fingermarks. We found that two-photon imaging provides a significant advantage when dealing with fingermarks on high contrast backgrounds like aluminum cans. I was also a part of other nonlinear optics based research projects including, two-photon spectroscopy, ultrafast photochemistry characterization, and two-photon microscopy.

Repasky Lab

In Dr. Kevin Repasky's lab I worked on the LabVIEW instrument control and MATLAB data analysis software for a micro-pulsed LIDAR system. This system was used to measure aerosols for atmospheric studies. I worked on automating the data acquisition using LabVIEW and improving the MATLAB code, which analyzed the laser backscatter data.

Spectrum Lab

My undergraduate research consisted of advancing a laser system for remote sensing of chemicals, using differential absorption LIDAR (DIAL) in the mid-IR (3-4 um range). I was responsible for characterizing and optimizing a Mono-Block Nd:YAG laser resonator (from Scientific Materials) and the associated optical parametric amplification system used to achieve a tunable pulsed NIR output.

All Publications

A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues

Glaser, Adam K., Bishop, Kevin W., Barner, Lindsey A., Susaki, Etsuo A., Kubota, Shimpei I., Gao, Gan, Serafin, Robert B., Balaram, Pooja, Turschak, Emily, Nicovich, Philip R., Lai, Hoyin, Lucas, Luciano A. G., Yi, Yating, Nichols, Eva K., Huang, Hongyi, Reder, Nicholas P., Wilson, Jasmine J., Sivakumar, Ramya, Shamskhou, Elya, Stoltzfus, Caleb R., Wei, Xing, Hempton, Andrew K., Pende, Marko, Murawala, Prayag, Dodt, Hans-Ulrich, Imaizumi, Takato, Shendure, Jay, Beliveau, Brian J., Gerner, Michael Y., Xin, Li, Zhao, Hu, True, Lawrence D., Reid, Clay R., Chandrashekar, Jayaram, Ueda, Hiroki R., Svoboda, Karel, Lui, Jonathan T.C. "A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues." Nature Methods 19, no. 5 (2022): 613-619.

Multi-Parameter Quantitative Imaging of Tumor Microenvironments Reveals Perivascular Immune Niches Associated with Anti-Tumor Immunity

Caleb R Stoltzfus, Ramya Sivakumar, Leo Kunz, Brandy E Olin Pope, Elena Menietti, Dario Speziale, Roberto Adelfio, Marina Bacac, Sara Colombetti, Mario Perro, Michael Y Gerner "Multi-Parameter Quantitative Imaging of Tumor Microenvironments Reveals Perivascular Immune Niches Associated with Anti-Tumor Immunity" bioRxiv 2021.06.17.448881; doi: https://doi.org/10.1101/2021.06.17.448881

TGFβ restricts expansion, survival, and function of T cells within the tuberculous granuloma

Gern, Benjamin H., Adams, Kristin N., Plumlee, Courtney R., Stoltzfus, Caleb R., Shehata, Laila, Moguche, Albanus O., Busman-Sahay, Kathleen et al. "TGFβ restricts expansion, survival, and function of T cells within the tuberculous granuloma." Cell Host & Microbe (2021).

Innate cell microenvironments in lymph nodes shape the generation of T cell responses during type I inflammation

Leal, Joseph M., Huang, Jessica Y., Kohli, Karan, Stoltzfus, Caleb R., Lyons-Cohen, Miranda R., Olin, Brandy E., Gale Jr., Michael, Gerner, Michael Y. "Innate cell microenvironments in lymph nodes shape the generation of T cell responses during type I inflammation" Science Immunology 6, no. 56 (2021): eabb9435

Ultra-low Dose Aerosol Infection of Mice with Mycobacterium tuberculosis More Closely Models Human Tuberculosis

Plumlee, Courtney R., Duffy, Fergal J., Gern, Benjamin H., Delahaye, Jared L., Cohen, Sara B., Stoltzfus, Caleb R., Rustad, Tige R. et al. "Ultra-low Dose Aerosol Infection of Mice with Mycobacterium tuberculosis More Closely Models Human Tuberculosis" Cell Host & Microbe 29, no. 1 (2021): 68-82.

CytoMAP: A Spatial Analysis Toolbox Reveals Features of Myeloid Cell Organization in Lymphoid Tissues

Stoltzfus, Caleb R., Filipek, Jakub, Gern, Benjamin H., Olin, Brandy E., Leal, Joseph M., Wu, Yajun, Lyons-Cohen, Miranda R. et al. "CytoMAP: a spatial analysis toolbox reveals features of myeloid cell organization in lymphoid tissues." Cell Reports 31, no. 3 (2020): 107523.

Multi-Immersion Open-Top Light-Sheet Microscope for High-Throughput Imaging of Cleared Tissues

Glaser, Adam K., Reder, Nicholas P., Chen, Ye, Yin, Chengbo, Wei, Linpeng, Kang, Soyoung, Barner, Lindsey A. et al. "Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues." Nature Communications 10, no. 1 (2019): 1-8.

Micro-Sized Tunable Liquid Crystal Optical Filters

Stoltzfus, Caleb, Russell Barbour, David Atherton, and Zeb Barber. "Micro-sized tunable liquid crystal optical filters." Optics Letters 42, no. 11 (2017): 2090-2093.

Optimizing Ultrafast Wide Field-of-View Illumination for High-Throughput Multi-Photon Imaging and Screening of Mutant Fluorescent Proteins

Stoltzfus, Caleb, Alexandr Mikhailov, and Aleksander Rebane. "Optimizing ultrafast wide field-of-view illumination for high-throughput multi-photon imaging and screening of mutant fluorescent proteins." In Multiphoton Microscopy in the Biomedical Sciences XVII, vol. 10069, p. 1006924. International Society for Optics and Photonics, 2017.

Wide Field-of-View Two-Photon Excited Fluorescence Imaging, Theory and Applications

Stoltzfus, Caleb Ray. "Wide field of view two-photon excited fluorescence imaging, theory and applications." PhD diss., Montana State University-Bozeman, College of Letters & Science, 2016.

High Contrast Two-Photon Imaging of Fingermarks

Stoltzfus, Caleb R., and Aleksander Rebane. "High contrast two-photon imaging of fingermarks." Scientific Reports 6, no. 1 (2016): 1-4.

Optimizing Ultrafast Illumination for Multiphoton-Excited Fluorescence Imaging

Stoltzfus, Caleb R., and Aleksander Rebane. "Optimizing ultrafast illumination for multiphoton-excited fluorescence imaging." Biomedical Optics Express 7, no. 5 (2016): 1768-1782.

Long- and Short-Range Electrostatic Fields in GFP Mutants: Implications for Spectral Tuning

Drobizhev, M., P. R. Callis, R. Nifosì, G. Wicks, C. Stoltzfus, L. Barnett, T. E. Hughes, P. Sullivan, and A. Rebane. "Long-and short-range electrostatic fields in GFP mutants: Implications for spectral tuning." Scientific Reports 5, no. 1 (2015): 1-14.

Two-Photon Directed Evolution of Green Fluorescent Proteins

Stoltzfus, Caleb R., Lauren M. Barnett, Mikhail Drobizhev, Geoffrey Wicks, Alexander Mikhaylov, Thomas E. Hughes, and Aleksander Rebane. "Two-photon directed evolution of green fluorescent proteins." Scientific Reports 5 (2015): 11968.

Multiphoton Photochemistry of Red Fluorescent Proteins in Solution and Live Cells

Drobizhev, Mikhail, Caleb Stoltzfus, Igor Topol, Jack Collins, Geoffrey Wicks, Alexander Mikhaylov, Lauren Barnett, Thomas E. Hughes, and Aleksander Rebane. "Multiphoton photochemistry of red fluorescent proteins in solution and live cells." The Journal of Physical Chemistry B 118, no. 31 (2014): 9167-9179.

A Multidimensional Screening Method for the Selection of Two-Photon Enhanced Fluorescent Proteins

Stoltzfus, Caleb, Lauren Barnett, Aleksander Rebane, Thomas Hughes, Mikhail Drobizhev, Geoffrey Wicks, and Alexandr Mikhailov. "A multidimensional screening method for the selection of two-photon enhanced fluorescent proteins." In Reporters, Markers, Dyes, Nanoparticles, and Molecular Probes for Biomedical Applications VI, vol. 8956, p. 895611. International Society for Optics and Photonics, 2014.

The Two-Photon Bazooka: A New Way of Optically Screening Randomly Mutagenized Libraries of Fluorescent Proteins

Barnett, Lauren M., Caleb Stoltzfus, Geoffrey Wicks, Mikhail Drobizhev, Alexandr Mikhailov, Aleksander Rebane, and Thomas E. Hughes. "The two-photon bazooka: A new way of optically screening randomly mutagenized libraries of fluorescent proteins." Biophysical Journal 106, no. 2 (2014): 810a-811a.

Mechanisms of Multiphoton Bleaching of Red Fluorescent Proteins

Drobizhev, Mikhail, Caleb Stoltzfus, Thomas Hughes, Igor Topol, Lauren M. Barnett, Geoffrey R. Wicks, and Aleksander Rebane. "Mechanisms of Multiphoton Bleaching of Red Fluorescent Proteins." Biophysical Journal 106, no. 2 (2014): 607a.