Scott E Fraser, PhD

Fraser Lab Website

Professor Scott E. Fraser has a long-standing commitment to quantitative biology, applying the tools of chemistry, engineering and physics to problems in biology and medicine. His personal research centers on imaging and molecular analyses of intact biological systems, with an emphasis on early development, organogenesis, and medical diagnostics. After training in physics (BS, Harvey Mudd College, 1976) and biophysics (PhD, Johns Hopkins University, 1979), he joined the faculty at UC Irvine, and rose through the ranks to become Chair of the Department of Physiology and Biophysics. In 1990 he moved to Caltech to serve as the Anna L. Rosen Professor of Biology, and the Director of the Biological Imaging Center. He is deeply committed to interdisciplinary training and translational research, having helped found the Caltech Brain Imaging Center and the Kavli Institute of Nanoscience, as well as serving as the Director of the Rosen Center for Biological Engineering. In Fall 2012, he moved to USC to take a Provost Professorship in the Dornsife College of Letters, Arts and Sciences, the Children’s Hospital Los Angeles, Keck School of Medicine and the Viterbi School of Engineering. He remains active in interdisciplinary research and serves as the Director of Science Initiatives for the USC campuses.

• In vivo Imaging of the Human Retina at the Molecular Level
  NIH · R01EY032994 · Mar 1, 2024 – Feb 29, 2028 · Role: Co-Principal Investigator
• Early tumorigenesis in vivo imaging, scRNA-seq to functional assays
  NIH · R21CA267849 · Dec 13, 2021 – Nov 30, 2023 · Role: Co-Principal Investigator
• Circuits underlying threat and safety
  NIH · U01NS122082 · Apr 15, 2021 – Mar 31, 2024 · Role: Co-Principal Investigator
• In vivo imaging of tumor heterogeneity generation from endogenous single cells
  NIH · R21CA209012 · Jul 1, 2016 – Jun 30, 2019 · Role: Principal Investigator
• Dynamic mapping of the complete synaptome using recombinant probes
  NIH · R01MH107238 · Sep 25, 2014 – Jul 31, 2020 · Role: Co-Principal Investigator
• Phase Contrast OCT for Non-Invasive Imaging of Retinovascular Disease
  NIH · R42EY021054 · Sep 30, 2010 – May 31, 2016 · Role: Principal Investigator
• Characterization of Exudative Macular Degeneration and Diabetic Retinopathy Using
  NIH · R41EY021054 · Sep 30, 2010 – Jun 29, 2012 · Role: Principal Investigator
• Functional analysis of neural crest & palate: Imaging craniofacial development
  NIH · U01DE020063 · Sep 21, 2009 – Apr 30, 2014 · Role: Principal Investigator
• Center for in Toto Genomic Analysis of Vertebrate Development
  NIH · P50HG004071 · Aug 15, 2006 – Jul 31, 2012 · Role: Principal Investigator
• Hemodynamic Forces in Vascular Remodeling
  NIH · R01HL078694 · Sep 22, 2004 – Aug 31, 2008 · Role: Principal Investigator
• Intravital imaging of neuronal development
  NIH · R01HD043897 · Jan 15, 2003 – Jan 14, 2007 · Role: Principal Investigator
• Santa Cruz Meeting on Developmental Biology
  NIH · R13HD042812 · Jun 5, 2002 – May 31, 2003 · Role: Principal Investigator
• OPTIC NERVE DEMYELINATION STUDY USING MRI
  NIH · R01EY011933 · Sep 30, 1999 – Sep 29, 2003 · Role: Principal Investigator
• GORDON CONFERENCE ON DEVELOPMENTAL BIOLOGY
  NIH · R13HD033376 · Jul 27, 1995 – Jun 30, 1996 · Role: Principal Investigator
• CELLULAR BASES OF COCAINE-INDUCED BRAIN ABNORMALITIES
  NIH · R55DA008689 · Sep 30, 1993 – Aug 31, 1995 · Role: Principal Investigator
• VITAL DYE ANALYSIS OF HINDBRAIN DEVELOPMENT
  NIH · R01HD029304 · Sep 1, 1991 – Aug 31, 1996 · Role: Principal Investigator
• DYNAMIC ASPECTS OF NEURONAL PATTERNING
  NIH · R01EY008363 · Dec 1, 1989 – Nov 30, 1992 · Role: Principal Investigator
• FUNCTIONAL RECONSTRUCTION OF NEURONAL SYSTEMS
  NIH · R01NS025210 · Sep 1, 1987 – Aug 31, 1990 · Role: Principal Investigator

• Negative-Valence Neurons in the Larval Zebrafish Pallium. bioRxiv. 2026 Feb 20.. View in PubMed
• Ultra-Sensitive Detection of Phytophthora pluvialis by Real-Time PCR Targeting a Mitochondrial Gene. Phytopathology. 2026 Jan; 116(1):51-62.. View in PubMed
• Transforming hyperspectral data into insight: the DREAM approach for pathology. Biomed Opt Express. 2025 Nov 01; 16(11):4420-4437.. View in PubMed
• Lack of Williams syndrome-associated genes alters quantity discrimination in zebrafish. Behav Brain Res. 2026 01 05; 496:115860.. View in PubMed
• Numerical discrimination in Danionella. iScience. 2025 Nov 21; 28(11):113667.. View in PubMed
• Far-red chemigenetic kinase biosensors enable multiplexed and super-resolved imaging of signaling networks. Nat Biotechnol. 2026 Mar; 44(3):444-453.. View in PubMed
• Subcellular Compartmentalization of Glucose Mediated Insulin Secretion. Cells. 2025 01 29; 14(3).. View in PubMed
• Rapid diffused optical imaging for accurate 3D estimation of subcutaneous tissue features. iScience. 2025 Feb 21; 28(2):111818.. View in PubMed
• Decoding Insulin Secretory Granule Maturation Using Genetically Encoded pH Sensors. ACS Sens. 2024 11 22; 9(11):6032-6039.. View in PubMed
• Neural Basis of Number Sense in Larval Zebrafish. bioRxiv. 2024 Sep 05.. View in PubMed
• Insulator-based dielectrophoresis-assisted separation of insulin secretory vesicles. Elife. 2024 Aug 27; 13.. View in PubMed
• METAPHOR: Metabolic evaluation through phasor-based hyperspectral imaging and organelle recognition for mouse blastocysts and oocytes. Proc Natl Acad Sci U S A. 2024 Jul 09; 121(28):e2315043121.. View in PubMed
• Label-free metabolic optical biomarkers track stem cell fate transition in real time. Sci Adv. 2024 05 10; 10(19):eadi6770.. View in PubMed
• More than double the fun with two-photon excitation microscopy. Commun Biol. 2024 03 26; 7(1):364.. View in PubMed
• Far-red chemigenetic biosensors for multi-dimensional and super-resolved kinase activity imaging. bioRxiv. 2024 Feb 11.. View in PubMed
• SHR and SCR coordinate root patterning and growth early in the cell cycle. Nature. 2024 02; 626(7999):611-616.. View in PubMed
• Scaling up polarized RPE cell supernatant production on parylene membrane. Exp Eye Res. 2024 03; 240:109789.. View in PubMed
• Episodic live imaging of cone photoreceptor maturation in GNAT2-EGFP retinal organoids. Dis Model Mech. 2023 11 01; 16(11).. View in PubMed
• Hand2 represses non-cardiac cell fates through chromatin remodeling at cis- regulatory elements. bioRxiv. 2023 Sep 24.. View in PubMed
• VoDEx: a Python library for time annotation and management of volumetric functional imaging data. Bioinformatics. 2023 09 02; 39(9).. View in PubMed
• Application of fluorescence lifetime imaging microscopy to monitor glucose metabolism in pancreatic islets in vivo. Biomed Opt Express. 2023 Aug 01; 14(8):4170-4178.. View in PubMed
• Development of Highly Fluorogenic Styrene Probes for Visualizing RNA in Live Cells. ACS Chem Biol. 2023 07 21; 18(7):1523-1533.. View in PubMed
• VoDEx: a Python library for time annotation and management of volumetric functional imaging data. ArXiv. 2023 May 11.. View in PubMed
• A single-shot hyperspectral phasor camera for fast, multi-color fluorescence microscopy. Cell Rep Methods. 2023 04 24; 3(4):100441.. View in PubMed
• Episodic live imaging of cone photoreceptor maturation in GNAT2-EGFP retinal organoids. bioRxiv. 2023 Mar 01.. View in PubMed
• HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal-to-noise fluorescence. Nat Methods. 2023 02; 20(2):248-258.. View in PubMed
• Cilia function as calcium-mediated mechanosensors that instruct left-right asymmetry. Science. 2023 01 06; 379(6627):71-78.. View in PubMed
• The kinase occupancy of T cell coreceptors reconsidered. Proc Natl Acad Sci U S A. 2022 12 06; 119(49):e2213538119.. View in PubMed
• baz1b loss-of-function in zebrafish produces phenotypic alterations consistent with the domestication syndrome. iScience. 2023 Jan 20; 26(1):105704.. View in PubMed
• Kinetic and data-driven modeling of pancreatic β-cell central carbon metabolism and insulin secretion. PLoS Comput Biol. 2022 10; 18(10):e1010555.. View in PubMed
• Extended depth-of-field light-sheet microscopy improves imaging of large volumes at high numerical aperture. Appl Phys Lett. 2022 Oct 17; 121(16):163701.. View in PubMed
• FRaeppli: a multispectral imaging toolbox for cell tracing and dense tissue analysis in zebrafish. Development. 2022 08 15; 149(16).. View in PubMed
• Sharing Begins at Home: How Continuous and Ubiquitous FAIRness Can Enhance Research Productivity and Data Reuse. Harv Data Sci Rev. 2022; 4(3).. View in PubMed
• Insights into Metabolic Activity and Structure of the Retina through Multiphoton Fluorescence Lifetime Imaging Microscopy in Mice. Cells. 2022 07 22; 11(15).. View in PubMed
• Quantity as a Fish Views It: Behavior and Neurobiology. Front Neuroanat. 2022; 16:943504.. View in PubMed
• Art centres supporting our Elders – ‘old people, that’s where our strength comes from’ – results from a national survey of Australian Aboriginal and Torres Strait Islander community controlled art centres. Rural Remote Health. 2022 05; 22(2):6850.. View in PubMed
• Publisher Correction: Author Correction: High-contrast, synchronous volumetric imaging with selective volume illumination microscopy. Commun Biol. 2022 May 27; 5(1):533.. View in PubMed
• A Novel Egg-In-Cube System Enables Long-Term Culture and Dynamic Imaging of Early Embryonic Development. Front Physiol. 2022; 13:893736.. View in PubMed
• Author Correction: High-contrast, synchronous volumetric imaging with selective volume illumination microscopy. Commun Biol. 2022 Apr 11; 5(1):363.. View in PubMed
• Bladder cancer cells shift rapidly and spontaneously to cisplatin-resistant oxidative phosphorylation that is trackable in real time. Sci Rep. 2022 04 01; 12(1):5518.. View in PubMed
• Characterizing ontogeny of quantity discrimination in zebrafish. Proc Biol Sci. 2022 02 09; 289(1968):20212544.. View in PubMed
• Regional synapse gain and loss accompany memory formation in larval zebrafish. Proc Natl Acad Sci U S A. 2022 01 18; 119(3).. View in PubMed
• Neurons in the Dorso-Central Division of Zebrafish Pallium Respond to Change in Visual Numerosity. Cereb Cortex. 2022 01 10; 32(2):418-428.. View in PubMed
• SARS-CoV2 infects pancreatic beta cells in vivo and induces cellular and subcellular disruptions that reflect beta cell dysfunction. Res Sq. 2021 Jul 20.. View in PubMed
• Single-objective selective-volume illumination microscopy enables high-contrast light-field imaging. Opt Lett. 2021 Jun 15; 46(12):2860-2863.. View in PubMed
• Live-cell imaging of glucose-induced metabolic coupling of β and α cell metabolism in health and type 2 diabetes. Commun Biol. 2021 05 19; 4(1):594.. View in PubMed
• Complex wavelet filter improves FLIM phasors for photon starved imaging experiments. Biomed Opt Express. 2021 Jun 01; 12(6):3463-3473.. View in PubMed
• Robust Multichannel Encoding for Highly Multiplexed Quantitative PCR. Anal Chem. 2021 03 09; 93(9):4208-4216.. View in PubMed
• Label-Free Visualization and Tracking of Gold Nanoparticles in Vasculature Using Multiphoton Luminescence. Nanomaterials (Basel). 2020 Nov 12; 10(11).. View in PubMed
• A versatile, multi-laser twin-microscope system for light-sheet imaging. Rev Sci Instrum. 2020 May 01; 91(5):053703.. View in PubMed
• Response to change in the number of visual stimuli in zebrafish:A behavioural and molecular study. Sci Rep. 2020 04 01; 10(1):5769.. View in PubMed
• A standard set of person-centred outcomes for diabetes mellitus: results of an international and unified approach. Diabet Med. 2020 12; 37(12):2009-2018.. View in PubMed
• High-contrast, synchronous volumetric imaging with selective volume illumination microscopy. Commun Biol. 2020 02 14; 3(1):74.. View in PubMed
• Pre-processing visualization of hyperspectral fluorescent data with Spectrally Encoded Enhanced Representations. Nat Commun. 2020 02 05; 11(1):726.. View in PubMed
• Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair. Nat Commun. 2020 01 30; 11(1):600.. View in PubMed
• Non-invasive Optical Biomarkers Distinguish and Track the Metabolic Status of Single Hematopoietic Stem Cells. iScience. 2020 Feb 21; 23(2):100831.. View in PubMed
• MEASUREMENT OF THE HYDRAULIC CONDUCTIVITY OF THE VITREOUS HUMOR. J Porous Media. 2020; 23(2):195-206.. View in PubMed
• Doctors’ perspectives on adhering to advance care directives when making medical decisions for patients: an Australian interview study. BMJ Open. 2019 10 31; 9(10):e032638.. View in PubMed
• Inhibition of nucleotide synthesis promotes replicative senescence of human mammary epithelial cells. J Biol Chem. 2019 07 05; 294(27):10564-10578.. View in PubMed
• Resilient Graphene Ultrathin Flat Lens in Aerospace, Chemical, and Biological Harsh Environments. ACS Appl Mater Interfaces. 2019 Jun 05; 11(22):20298-20303.. View in PubMed
• Diffusive Transport in the Vitreous Humor: Experimental and Analytical Studies. J Heat Transfer. 2019 May; 141(5):050801.. View in PubMed
• Using enhanced number and brightness to measure protein oligomerization dynamics in live cells. Nat Protoc. 2019 02; 14(2):616-638.. View in PubMed
• Significant Expansion of Real-Time PCR Multiplexing with Traditional Chemistries using Amplitude Modulation. Sci Rep. 2019 01 31; 9(1):1053.. View in PubMed
• Discs large 1 controls daughter-cell polarity after cytokinesis in vertebrate morphogenesis. Proc Natl Acad Sci U S A. 2018 11 13; 115(46):E10859-E10868.. View in PubMed
• Canadian Surgery Forum 2018: St. John’s, NL Sept. 13-15, 2018. Can J Surg. 2018 Aug; 61(4 Suppl 1):S94-S174.. View in PubMed
• Fiber pattern removal and image reconstruction method for snapshot mosaic hyperspectral endoscopic images. Biomed Opt Express. 2018 Feb 01; 9(2):780-790.. View in PubMed
• Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos. Development. 2018 01 08; 145(1).. View in PubMed
• Eph-ephrin signaling modulated by polymerization and condensation of receptors. Proc Natl Acad Sci U S A. 2017 12 12; 114(50):13188-13193.. View in PubMed
• Genetic and neuronal regulation of sleep by neuropeptide VF. Elife. 2017 11 06; 6.. View in PubMed
• Multi-shaping technique reduces sidelobe magnitude in optical coherence tomography. Biomed Opt Express. 2017 Nov 01; 8(11):5267-5281.. View in PubMed
• SERCA directs cell migration and branching across species and germ layers. Biol Open. 2017 Oct 15; 6(10):1458-1471.. View in PubMed
• Using a linked database for epidemiology across the primary and secondary care divide: acute kidney injury. BMC Med Inform Decis Mak. 2017 Jul 11; 17(1):106.. View in PubMed
• Structural and Functional Characterization of Human Stem-Cell-Derived Retinal Organoids by Live Imaging. Invest Ophthalmol Vis Sci. 2017 07 01; 58(9):3311-3318.. View in PubMed
• 3D in vivo imaging with extended-focus optical coherence microscopy. J Biophotonics. 2017 Nov; 10(11):1411-1420.. View in PubMed
• Biotagging of Specific Cell Populations in Zebrafish Reveals Gene Regulatory Logic Encoded in the Nuclear Transcriptome. Cell Rep. 2017 04 11; 19(2):425-440.. View in PubMed
• Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging. Nat Methods. 2017 02; 14(2):149-152.. View in PubMed
• Phase variance optical coherence microscopy for label-free imaging of the developing vasculature in zebrafish embryos. J Biomed Opt. 2016 12 01; 21(12):126022.. View in PubMed
• Macrophage Epithelial Reprogramming Underlies Mycobacterial Granuloma Formation and Promotes Infection. Immunity. 2016 10 18; 45(4):861-876.. View in PubMed
• Mapping a multiplexed zoo of mRNA expression. Development. 2016 10 01; 143(19):3632-3637.. View in PubMed
• Conditional Creation and Rescue of Nipbl-Deficiency in Mice Reveals Multiple Determinants of Risk for Congenital Heart Defects. PLoS Biol. 2016 09; 14(9):e2000197.. View in PubMed
• An E3-ligase-based method for ablating inhibitory synapses. Nat Methods. 2016 08; 13(8):673-8.. View in PubMed
• Intracellular kinetics of the androgen receptor shown by multimodal Image Correlation Spectroscopy (mICS). Sci Rep. 2016 Mar 03; 6:22435.. View in PubMed
• Imaging of the cross-presenting dendritic cell subsets in the skin-draining lymph node. Proc Natl Acad Sci U S A. 2016 Jan 26; 113(4):1044-9.. View in PubMed
• Characterization of Antibody Bipolar Bridging Mediated by the Human Cytomegalovirus Fc Receptor gp68. J Virol. 2016 Jan 06; 90(6):3262-7.. View in PubMed
• Tools for the Microbiome: Nano and Beyond. ACS Nano. 2016 Jan 26; 10(1):6-37.. View in PubMed
• Imaging the Cell and Molecular Dynamics of Craniofacial Development: Challenges and New Opportunities in Imaging Developmental Tissue Patterning. Curr Top Dev Biol. 2015; 115:599-629.. View in PubMed
• Nanobody-targeted E3-ubiquitin ligase complex degrades nuclear proteins. Sci Rep. 2015 Sep 16; 5:14269.. View in PubMed
• A transgenic quail model that enables dynamic imaging of amniote embryogenesis. Development. 2015 Aug 15; 142(16):2850-9.. View in PubMed
• Detection of pigment epithelial detachment vascularization in age-related macular degeneration using phase-variance OCT angiography. Clin Ophthalmol. 2015; 9:1299-305.. View in PubMed
• Spatio-Temporal Differences in Dystrophin Dynamics at mRNA and Protein Levels Revealed by a Novel FlipTrap Line. PLoS One. 2015; 10(6):e0128944.. View in PubMed
• Dynamic structure and protein expression of the live embryonic heart captured by 2-photon light sheet microscopy and retrospective registration. Biomed Opt Express. 2015 Jun 01; 6(6):2056-66.. View in PubMed
• Dynamic imaging of the growth plate cartilage reveals multiple contributors to skeletal morphogenesis. Nat Commun. 2015 Apr 13; 6:6798.. View in PubMed
• Combinatorial analysis of mRNA expression patterns in mouse embryos using hybridization chain reaction. Cold Spring Harb Protoc. 2015 Mar 02; 2015(3):259-68.. View in PubMed
• Airway branching has conserved needs for local parasympathetic innervation but not neurotransmission. BMC Biol. 2014 Nov 11; 12:92.. View in PubMed
• Abundance of gap junctions at glutamatergic mixed synapses in adult Mosquitofish spinal cord neurons. Front Neural Circuits. 2014; 8:66.. View in PubMed
• The herpes virus Fc receptor gE-gI mediates antibody bipolar bridging to clear viral antigens from the cell surface. PLoS Pathog. 2014 Mar; 10(3):e1003961.. View in PubMed
• Efficient generation of transgenic mice by lentivirus-mediated modification of spermatozoa. FASEB J. 2014 Feb; 28(2):569-76.. View in PubMed
• Phase-variance optical coherence tomography: a technique for noninvasive angiography. Ophthalmology. 2014 Jan; 121(1):180-187.. View in PubMed
• A detailed description of an economical setup for electroporation of chick embryos in ovo. Braz J Med Biol Res. 2013 Sep; 46(9):752-7.. View in PubMed
• Optical imaging of the chorioretinal vasculature in the living human eye. Proc Natl Acad Sci U S A. 2013 Aug 27; 110(35):14354-9.. View in PubMed

• Crump, Gage
• Chai, Yang
• Chuong, Cheng-Ming
• Toga, Arthur
• Thompson, Paul
• Nayak, Krishna