Prof. Scott S. Howard Profile

Prof. Scott S. Howard

Associate Professor at Univ of Notre Dame

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Author

Publications (23)

Proceedings Article | 25 April 2023 Presentation + Paper

3D time resolved multiphoton fluorescence lifetime imaging microscopy of nano-crystalline agricultural treatments on living plant tissue

Xiaotong Yuan, Varun Mannam, Scott Howard

Proceedings Volume 12384, 123840A (2023) https://doi.org/10.1117/12.2650736

KEYWORDS: Tissues, Agriculture, Fluorescence lifetime imaging, 3D image processing, Biological imaging, Biological samples, Multiphoton fluorescence microscopy, Fluorescence imaging, Proteins, Molecular imaging

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SPIE Journal Paper | 14 March 2023 Open Access

Small training dataset convolutional neural networks for application-specific super-resolution microscopy

Varun Mannam, Scott Howard

JBO, Vol. 28, Issue 03, 036501, (March 2023) https://doi.org/10.1117/12.10.1117/1.JBO.28.3.036501

KEYWORDS: Education and training, Image analysis, Data modeling, Convolutional neural networks, Fluorescence microscopy, Gallium nitride, Point spread functions, Performance modeling, Lawrencium, Network architectures

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SignificanceMachine learning (ML) models based on deep convolutional neural networks have been used to significantly increase microscopy resolution, speed [signal-to-noise ratio (SNR)], and data interpretation. The bottleneck in developing effective ML systems is often the need to acquire large datasets to train the neural network. We demonstrate how adding a “dense encoder-decoder” (DenseED) block can be used to effectively train a neural network that produces super-resolution (SR) images from conventional microscopy diffraction-limited (DL) images trained using a small dataset [15 fields of view (FOVs)].AimThe ML helps to retrieve SR information from a DL image when trained with a massive training dataset. The aim of this work is to demonstrate a neural network that estimates SR images from DL images using modifications that enable training with a small dataset.ApproachWe employ “DenseED” blocks in existing SR ML network architectures. DenseED blocks use a dense layer that concatenates features from the previous convolutional layer to the next convolutional layer. DenseED blocks in fully convolutional networks (FCNs) estimate the SR images when trained with a small training dataset (15 FOVs) of human cells from the Widefield2SIM dataset and in fluorescent-labeled fixed bovine pulmonary artery endothelial cells samples.ResultsConventional ML models without DenseED blocks trained on small datasets fail to accurately estimate SR images while models including the DenseED blocks can. The average peak SNR (PSNR) and resolution improvements achieved by networks containing DenseED blocks are ≈3.2 dB and 2 × , respectively. We evaluated various configurations of target image generation methods (e.g., experimentally captured a target and computationally generated target) that are used to train FCNs with and without DenseED blocks and showed that including DenseED blocks in simple FCNs outperforms compared to simple FCNs without DenseED blocks.ConclusionsDenseED blocks in neural networks show accurate extraction of SR images even if the ML model is trained with a small training dataset of 15 FOVs. This approach shows that microscopy applications can use DenseED blocks to train on smaller datasets that are application-specific imaging platforms and there is promise for applying this to other imaging modalities, such as MRI/x-ray, etc.

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Proceedings Article | 7 March 2023 Presentation + Paper

High-speed spatial parameter recovery using multi-distance frequency-domain diffuse optical spectroscopy

Robin Dale, Thomas O'Sullivan, Scott Howard, Chris Campbell, Felipe Orihuela-espina, Hamid Dehghani

Proceedings Volume 12376, 1237606 (2023) https://doi.org/10.1117/12.2651676

KEYWORDS: Tomography, Near infrared spectroscopy, Tissues, Signal attenuation, Optical properties, Tissue optics, Modulation frequency, Image resolution, Finite element methods, Scattering

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Proceedings Article | 7 March 2023 Presentation

Estimating the optical properties of multi-layered tissue models using structured interrogation frequency-domain near-infrared spectroscopy

Ola S. Abdalsalam, Thomas O'Sullivan, Scott Howard

Proceedings Volume PC12376, PC1237603 (2023) https://doi.org/10.1117/12.2650962

KEYWORDS: Optical properties, Near infrared spectroscopy, Tissue optics, Phase shift keying, Tissues, Phase measurement, Modulation, Light sources

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Proceedings Article | 4 March 2022 Presentation + Paper

Improved sensitivity to deep tissues using phase-based structured interrogation frequency-domain near-infrared spectroscopy

Ola Abdalsalam, Scott Howard, Thomas O'Sullivan

Proceedings Volume 11944, 119440A (2022) https://doi.org/10.1117/12.2609662

KEYWORDS: Diffuse optical imaging, Diffuse optical spectroscopy, Tissues, Optical properties, Phase measurement, Near infrared spectroscopy, Sensors, Absorption, Scattering, Phase shifts, Reflectivity, Modulation

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Proceedings Article | 4 March 2022 Presentation + Paper

Deconvolution of fluorescence lifetime imaging microscopy (FLIM)

Varun Mannam, Xiaotong Yuan, Scott Howard

Proceedings Volume 11965, 1196508 (2022) https://doi.org/10.1117/12.2608910

KEYWORDS: Fluorescence lifetime imaging, Deconvolution, Microscopy, Luminescence, Convolution, Point spread functions, Multiphoton microscopy, Multiphoton fluorescence microscopy, Image processing, Distortion

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Proceedings Article | 2 March 2022 Presentation + Paper

Low dosage 3D volume fluorescence microscopy imaging using compressive sensing

Varun Mannam, Jacob Brandt, Cody Smith, Scott Howard

Proceedings Volume 11966, 1196603 (2022) https://doi.org/10.1117/12.2607515

KEYWORDS: 3D image processing, Microscopy, Compressed sensing, Luminescence, In vivo imaging, Signal to noise ratio, Confocal microscopy, Reconstruction algorithms, Microscopes, 3D modeling

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Proceedings Article | 2 March 2022 Presentation

Instantaneous acquisition and analysis of intravital 3D fluorescence lifetime imaging microscopy

Scott Howard

Proceedings Volume PC11971, PC119710H (2022) https://doi.org/10.1117/12.2615412

KEYWORDS: Fluorescence lifetime imaging, Microscopy, 3D acquisition, 3D image processing, Multiphoton microscopy, Luminescence, In vivo imaging, 3D modeling, Tissues, Super resolution

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Proceedings Article | 5 March 2021 Presentation + Paper

Deep learning-based super-resolution fluorescence microscopy on small datasets

Varun Mannam, Yide Zhang, Xiaotong Yuan, Scott Howard

Proceedings Volume 11650, 116500O (2021) https://doi.org/10.1117/12.2578519

KEYWORDS: Super resolution, Microscopy, Luminescence, Organisms, Data modeling, X-rays, X-ray imaging, Visualization, Super resolution microscopy, Magnetic resonance imaging

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Proceedings Article | 5 March 2021 Poster + Presentation + Paper

Convolutional neural network denoising in fluorescence lifetime imaging microscopy (FLIM)

Varun Mannam, Yide Zhang, Xiaotong Yuan, Takashi Hato, Pierre Dagher, Evan Nichols, Cody Smith, Kenneth Dunn, Scott Howard

Proceedings Volume 11648, 116481C (2021) https://doi.org/10.1117/12.2578574

KEYWORDS: Fluorescence lifetime imaging, Image segmentation, Microscopy, Denoising, In vivo imaging, Luminescence, Convolutional neural networks, Signal to noise ratio, Imaging systems, Signal processing

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Proceedings Article | 5 March 2021 Presentation + Paper

Overcoming the fundamental limitation of frequency-domain fluorescence lifetime imaging microscopy spatial resolution

Xiaotong Yuan, Varun Mannam, Yide Zhang, Scott Howard

Proceedings Volume 11650, 116500M (2021) https://doi.org/10.1117/12.2577284

KEYWORDS: Fluorescence lifetime imaging, Microscopy, Super resolution, Spatial resolution, Luminescence, Stimulated emission depletion microscopy, Super resolution microscopy, Physics, Optical communications, Numerical simulations

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Proceedings Article | 1 March 2019 Paper

Self-calibrated frequency domain diffuse optical spectroscopy with a phased source array

Ola Abdalsalam, Yide Zhang, Scott Howard, Thomas O'Sullivan

Proceedings Volume 10874, 1087403 (2019) https://doi.org/10.1117/12.2510422

KEYWORDS: Tissues, Optical properties, Sensors, Modulation, Calibration, Scattering, Diffuse optical spectroscopy, Absorption, Light scattering, Diffusion

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Proceedings Article | 22 February 2019 Paper

Three-dimensional deep tissue multiphoton frequency-domain fluorescence lifetime imaging microscopy via phase multiplexing and adaptive optics

Yide Zhang, Ian Guldner, Evan Nichols, David Benirschke, Cody Smith, Siyuan Zhang, Scott Howard

Proceedings Volume 10882, 108822H (2019) https://doi.org/10.1117/12.2510674

KEYWORDS: Fluorescence lifetime imaging, Luminescence, 3D image processing, Multiplexing, Composites, Adaptive optics, Multiphoton microscopy, Phase shifts, Image filtering, Multiphoton fluorescence microscopy

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Proceedings Article | 22 February 2019 Presentation + Paper

Super-resolution multiphoton frequency-domain fluorescence lifetime imaging microscopy by generalized stepwise optical saturation (GSOS)

Yide Zhang, David Benirschke, Ola Abdalsalam, Scott Howard

Proceedings Volume 10884, 108840C (2019) https://doi.org/10.1117/12.2507663

KEYWORDS: Microscopy, Super resolution, Luminescence, Modulation, Fluorescence lifetime imaging, Multiphoton microscopy, Tissues, Point spread functions

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Proceedings Article | 9 October 2018 Presentation + Paper

Realization of a plug-and-play, low SWAP-C, MIR imaging system utilizing a commercially available low-cost VOx microbolometer array for enabling imaging applications

David Benirschke, Abbas Termos, Nikolaus Kleber, David Connelly, Bertrand Hochwald, Jonathan Chisum, Scott Howard

Proceedings Volume 10795, 107950D (2018) https://doi.org/10.1117/12.2325588

KEYWORDS: Imaging systems, Cameras, Microbolometers, Sensors, Imaging spectroscopy, Imaging arrays, Spectroscopy, Infrared spectroscopy, Infrared imaging, Camera shutters

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SPIE Journal Paper | 17 April 2017

Characterization of a low-cost, commercially available, vanadium oxide microbolometer array for spectroscopic imaging

David Benirschke, Scott Howard

OE, Vol. 56, Issue 04, 040502, (April 2017) https://doi.org/10.1117/12.10.1117/1.OE.56.4.040502

KEYWORDS: Imaging spectroscopy, Spectroscopy, Microbolometers, Imaging arrays, Long wavelength infrared, Temperature metrology, Vanadium, Oxides, Thermography, Quantum cascade lasers

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Proceedings Article | 27 September 2016 Presentation + Paper

Feasibility study of mid-infrared absorption spectroscopy using electrospray ionization

Tahsin Ahmed, Erick Foster, Paul Bohn, Scott Howard

Proceedings Volume 9930, 99300U (2016) https://doi.org/10.1117/12.2237958

KEYWORDS: Mid-IR, Absorption spectroscopy, Ionization, Quantum cascade lasers, Molecules, Explosives, Molecular spectroscopy, Liquids, FT-IR spectroscopy, Silicon

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SPIE Journal Paper | 4 June 2015 Open Access

Label-free and depth resolved optical sectioning of iron-complex deposits in sickle cell disease splenic tissue by multiphoton microscopy

Genevieve Vigil, Alexander Adami, Tahsin Ahmed, Aamir Khan, Sarah Chapman, Biree Andemariam, Roger Thrall, Scott Howard

JBO, Vol. 20, Issue 06, 066001, (June 2015) https://doi.org/10.1117/12.10.1117/1.JBO.20.6.066001

KEYWORDS: Single crystal X-ray diffraction, Tissues, Tissue optics, Spleen, Image segmentation, Iron, Image processing, Multiphoton microscopy, Biomedical optics, Luminescence

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Proceedings Article | 27 August 2014 Paper

Label free detection of phospholipids by infrared absorption spectroscopy

Tahsin Ahmed, Erick Foster, Genevieve Vigil, Aamir Khan, Paul Bohn, Scott Howard

Proceedings Volume 9166, 91660H (2014) https://doi.org/10.1117/12.2062094

KEYWORDS: Mid-IR, Absorption, Germanium, Microfluidics, Absorption spectroscopy, Infrared spectroscopy, Capillaries, Molecules, Antireflective coatings, Infrared detectors

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SPIE Journal Paper | 1 October 2013 Open Access

Two-photon fluorescence imaging of intracellular hydrogen peroxide with chemoselective fluorescent probes

Hengchang Guo, Hossein Aleyasin, Scott Howard, Bryan Dickinson, Vivian Lin, Chris Xu, Yu Chen, Rajiv Ratan, Renee Haskew-Layton

JBO, Vol. 18, Issue 10, 106002, (October 2013) https://doi.org/10.1117/12.10.1117/1.JBO.18.10.106002

KEYWORDS: Luminescence, Two photon imaging, Hydrogen, Absorption, Oxygen, Sapphire lasers, Confocal microscopy, Medical research, Molecules, In vivo imaging

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Proceedings Article | 11 September 2013 Paper

Nano-cone optical fiber array sensors for MiRNA profiling

Yunshan Wang, Satyajyoti Senapati, Paul Stoddart, Scott Howard, Hsueh-Chia Chang

Proceedings Volume 8812, 88120Q (2013) https://doi.org/10.1117/12.2023727

KEYWORDS: Sensors, Optical fibers, Plasmonics, Profiling, Gold, Cancer, Fluorescence resonance energy transfer, Microfluidics, Optical arrays, Luminescence

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Proceedings Article | 10 September 2013 Paper

FDTD modeling of chip-to-chip waveguide coupling via optical quilt packaging

Tahsin Ahmed, Thomas Butler, Aamir Khan, Jason Kulick, Gary Bernstein, Anthony Hoffman, Scott Howard

Proceedings Volume 8844, 88440C (2013) https://doi.org/10.1117/12.2024088

KEYWORDS: Waveguides, Quantum cascade lasers, Finite-difference time-domain method, Packaging, Integrated optics, Mid-IR, Waveguide modes, Copper, Semiconductors, Single mode fibers

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Proceedings Article | 8 February 2007 Paper

MOCVD growth and regrowth of quantum cascade lasers

Fow-Sen Choa, Liwei Cheng, Xiaoming Ji, Zhijun Liu, Daniel Wasserman, Scott Howard, Claire Gmachl, Xiaojun Wang, Jenyu Fan, Jacob Khurgin

Proceedings Volume 6485, 64850N (2007) https://doi.org/10.1117/12.714269

KEYWORDS: Quantum cascade lasers, Metalorganic chemical vapor deposition, Terahertz radiation, Oxides, Waveguides, Molybdenum, Mid-IR, Cladding, Etching, Interfaces

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Showing 5 of 23 publications

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