Double Helix Corporation

HIGH-RESOLUTION EXTENDED-DEPTH PHASE-ENGINEERED OBJECTIVES TO ACCELERATE SPATIAL 'OMICS R&D THROUGH COMPUTATIONAL OPTICS - 1 SUMMARY 2 THIS SBIR PHASE II PROJECT IS FOCUSED ON THE DEVELOPMENT AND VALIDATION OF GROUNDBREAKING ENGINEERED POINT 3 SPREAD FUNCTION (EPSF) MICROSCOPE OBJECTIVE LENSES (OL) THAT WILL EMPOWER THE NEXT GENERATION OF SPATIAL OMICS 4 INVESTIGATION. THE PROPOSED LINE OF EPSF-OL ADDRESSES THE CRITICAL NEED IN SPATIAL OMICS FOR RAPID HIGH-CONTENT 5 IMAGING TO FULLY CAPTURE CELLULAR IDENTITY. LEVERAGING THE POWER OF POINT SPREAD FUNCTION ENGINEERING TO EXTEND THE 6 DEPTH OF FIELD AND ENCODE 3D INFORMATION DIRECTLY INTO THE OPTICAL RESPONSE OF THE IMAGING SYSTEM ENABLES 7 VOLUMETRIC IMAGING WITH MANY FEWER AXIAL STEPS, SPEEDING IMAGE ACQUISITION, REDUCING DATASET SIZES, REDUCING 8 PHOTOTOXICITY AND PHOTODAMAGE, AND SHORTENING THE CYCLE TIME TO OBSERVE LIVE CELL DYNAMICS. ALL THESE BENEFITS 9 ARE ACHIEVED IN THE SAME FORM FACTOR AS STANDARD MICROSCOPE OBJECTIVE LENSES, WITHOUT REDUCING THE 10 NUMERICAL APERTURE (NA) OF THE SYSTEM, THUS PRESERVING HIGH RESOLUTION DATA CAPTURE. 11 DESPITE EXTRAORDINARY ADVANCES IN OPTICAL MICROSCOPY, STATE-OF-THE-ART SOLUTIONS HAVE BEEN SLOW TO MARKET, 12 LACKING IN FLEXIBILITY AND EASE OF ACCESS. THE EPSF-OL ARE BASED ON AN INTEGRATED DESIGN OF THE OBJECTIVE LENS, 13 PHASE MODULATION, AND RECOVERY SOFTWARE. SPECIFICALLY, TWO TYPES OF EPSF-OL WILL BE DEVELOPED – DEEP FOCUS 14 (DF) EPSF-OL EXTENDS THE DEPTH OF FIELD FOR VOLUMETRIC PROJECTION IMAGING, AND SINGLE HELIX (SH) EPSF-OL 15 EXTENDS THE DEPTH OF FIELD AND ENCODES 3D SPATIAL INFORMATION FOR FULL 3D IMAGING. RECOVERY SOFTWARE WILL TARGET 16 THE NEEDS OF SPATIAL OMICS – LOCALIZATION AND COUNTING OF BIOMOLECULES, AND EFFICIENT HIGH-RESOLUTION RESTORATION 17 OF SPATIAL CONTEXT FROM FEWER AXIAL SLICES. THE EPSF-OL WILL BE DESIGNED TO ACHIEVE THE SAME MAGNIFICATION, NA, 18 AND FIELD NUMBER AS POPULAR OBJECTIVE LENSES USED IN SPATIAL OMICS ASSAYS, THUS ACHIEVING PLUG-N-PLAY UPGRADE 19 COMPATIBILITY IN COMMERCIAL CLOSED-BOX, RESEARCH, OR LAB-BUILT OPTICAL MICROSCOPES. 20 THIS PROJECT TARGETS COMMERCIALIZATION OF COST-EFFECTIVE EPSF-OL OFFERED WITH NOVEL PHASE MODULATION MASKS 21 THAT EXTEND THE DEPTH OF FIELD UP TO 10 TIMES AS COMPARED TO STANDARD OBJECTIVE LENSES. THESE COMMERCIAL- 22 READY PROTOTYPES WILL INCLUDE A ROBUST OPTO-MECHANICAL DESIGN WITH EXCELLENT PERFORMANCE, SUPPORTED BY GPU 23 ACCELERATED AND AI-DRIVEN SOFTWARE. TESTS OF THE EPSF-OL AND SOFTWARE IN ADVANCED SPATIAL OMICS ASSAYS AT 24 PARTNER LABS WILL VALIDATE END-USER ACCEPTANCE AND PROVIDE VALUABLE FEEDBACK TOWARD COMMERCIALIZATION. 25 THE IMPLICATIONS IN SPATIAL OMICS ARE FAR-REACHING. FOR INSTANCE, THE EPSF-OL WILL BENEFIT THE STUDY OF 26 NEURODEGENERATIVE DISEASE, OWING TO THEIR ABILITY TO SIMULTANEOUSLY TRACK PROTEINS AND CAPTURE DIRECT QUANTITATIVE 27 READOUT OF TRANSCRIPTIONAL INDUCTION. THE EPSF-OL TECHNOLOGY WILL ALSO GREATLY ACCELERATE ERROR ROBUST 28 TRANSCRIPTIONAL SEQUENCING, HIGH CONTENT PROTEOMICS, AND THE STUDY OF EPIGENOMIC MARKERS. 29 DOUBLE HELIX OPTICS, A STARTUP WITH EXCLUSIVE RIGHTS TO THE EPSF TECHNOLOGY FROM U OF COLORADO, IS HEADQUARTERED 30 IN THE BIOFRONTIERS INSTITUTE IN BOULDER, CO, AND OPTIMALLY POSITIONED TO SUCCESSFULLY BRING THIS PRODUCT TO MARKET.

LIGHT ENGINEERING MODULE FOR FAST HIGH-RESOLUTION WHOLE-CELL IMAGING - SUMMARY THIS SBIR PHASE II PROJECT IS FOCUSED ON THE DESIGN REFINEMENT, DEVELOPMENT, AND TESTING OF A GROUND-BREAKING MULTIDIMENSIONAL MULTIFUNCTIONAL QUANTITATIVE OPTICAL MICROSCOPY MODULAR SYSTEM SUITABLE FOR LIVE WHOLE CELL STUDIES. THE PROPOSED LIGHT ENGINEERING MODULAR SYSTEM ADDRESSES THE CRITICAL NEED FOR FLEXIBLE IMAGING TECHNIQUES TO IMAGE LIVE WHOLE CELLS WITH LOW PHOTODAMAGE AND PHOTOTOXICITY WHILE PROVIDING HIGH SPATIAL AND TEMPORAL RESOLUTION AS WELL AS A LARGE VOLUMETRIC FIELD OF VIEW. DESPITE EXTRAORDINARY ADVANCES IN OPTICAL MICROSCOPY, THE AVAILABILITY OF STATE-OF-THE-ART COMMERCIAL SOLUTIONS HAS BEEN SLOW TO MARKET, LACKING IN FLEXIBILITY AND EASE OF ACCESS. THE MODULAR INSTRUMENT IS BASED ON AN INTEGRATED DESIGN OF THE ILLUMINATION, 3D OPTICAL RESPONSE, DATA COLLECTION, AND RECONSTRUCTION ALGORITHMS FOR FLUORESCENCE IMAGING. SPECIFICALLY, ENGINEERED 3D LIGHT EXCITATION LIMITS THE BACKGROUND NOISE WHILE REDUCING PHOTODAMAGE AND PHOTOTOXICITY. THE ENGINEERED 3D POINT SPREAD FUNCTIONS ENABLE MULTIPLEX FUNCTIONALITY INCLUDING AN EXTENDED DEPTH OF FIELD IMAGING, HIGH-SENSITIVITY 3D LOCALIZATION OF SINGLE-MOLECULES OR CELLULAR HETEROGENEITIES, MULTI-COLOR, AND 3D IMAGING. AS A RESULT, THE TARGET PERFORMANCE OUTPERFORMS THE STATE OF THE ART IN TERMS OF SPATIAL/TEMPORAL RESOLUTION, SIGNAL-TO-NOISE RATIO, FIELD OF VIEW, SINGLE-MOLECULE LOCALIZATION PRECISION, AND EASE OF USE. THIS PROJECT IS TARGETED TOWARDS COMMERCIALIZATION OF A COST-EFFECTIVE MODULAR SOLUTION THAT CAN BE EASILY INTEGRATED WITH EXISTING SCIENTIFIC MICROSCOPES. THE COMMERCIAL-READY PROTOTYPE, WILL INCLUDE A SMALL FOOTPRINT ARCHITECTURE, A SET OF NOVEL OPTICAL PHASE MASKS FOR POINT SPREAD FUNCTION ENGINEERING AND EXCITATION SHAPING, A ROBUST OPTOMECHANICAL DESIGN, AND REAL-TIME EXPERIMENT CONTROL SOFTWARE. TESTS OF THE INSTRUMENT IN SIGNIFICANT BIOMEDICAL PROBLEMS AT PARTNERS’ LABS WILL VALIDATE END-USER ACCEPTANCE AND PROVIDE VALUABLE FEEDBACK TOWARDS COMMERCIALIZATION. THE IMPLICATIONS IN BIOMEDICAL IMAGING ARE FAR-REACHING. FOR INSTANCE, THE INSTRUMENT WOULD BENEFIT THE STUDY OF ONCOGENESIS, OWING TO ITS DEGREE OF MOLECULAR SENSITIVITY FOR DETECTING THE SPATIAL LOCALIZATION OF RECEPTORS AND OTHER SIGNALING MOLECULES WITHIN THE TUMOR/EXTRACELLULAR MATRIX. IT WOULD ALSO EMPOWER THE STUDY OF DEGENERATIVE DISEASES WHERE THE INSTRUMENT CAN HELP REVEAL THEIR MOLECULAR ORIGIN AND DEVELOP NOVEL THERAPEUTIC STRATEGIES. THE NEW IMAGING CAPABILITIES COULD ALSO ADVANCE STEM CELL, CANCER AND BRAIN RESEARCH. DOUBLE HELIX OPTICS IS A STARTUP COMPANY WITH EXCLUSIVE LICENSING RIGHTS TO THE LIGHT ENGINEERING TECHNOLOGY FROM THE UNIVERSITY OF COLORADO, AS WELL AS THE NOVEL TETRAPOD AND MULTICOLOR PSF LOCALIZATION DEVELOPMENTS FROM STANFORD UNIVERSITY. THE COMPANY, HEADQUARTERED IN THE BIOFRONTIERS INSTITUTE IN BOULDER, IS OPTIMALLY POSITIONED TO SUCCESSFULLY BRING THIS PRODUCT TO MARKET.

SBIR PHASE II: THREE-DIMENSIONAL COMPUTATIONAL OPTICAL IMAGING SENSOR

SBIR PHASE II: WIDEFIELD THREE-DIMENSIONAL SUPERRESOLUTION MICROSCOPY MODULE

HIGH-RESOLUTION EXTENDED-DEPTH PHASE-ENGINEERED OBJECTIVES TO ACCELERATE SPATIAL 'OMICS R&D THROUGH COMPUTATIONAL OPTICS - SUMMARY THIS SBIR PHASE I PROJECT IS FOCUSED ON THE DESIGN, DEVELOPMENT, AND TESTING OF GROUNDBREAKING ENGINEERED POINT SPREAD FUNCTION (EPSF) OBJECTIVE LENSES, AND MATCHED COMPUTATIONAL ALGORITHMS FOR SPATIAL OMICS RESEARCH AND DEVELOPMENT, WHICH WILL BE SUITABLE FOR FIXED AND LIVE-CELL APPLICATIONS AND WILL ENABLE BREAKTHROUGHS IN FAST LIVE-CELL SPATIAL OMICS R&D BY INCREASING THE DEPTH OF FIELD, WITH HIGH-NA, FOR 3D VOLUMETRIC PROJECTION AND 3D VOLUME DATA CAPTURE. BY EXPLOITING DOUBLE HELIX OPTICS’ (DHO) LIGHT ENGINEERING™ TECHNOLOGY, WE WILL DESIGN, DEVELOP, AND VALIDATE ENGINEERED POINT SPREAD FUNCTION (EPSF) MICROSCOPE OBJECTIVE LENSES THAT EXTEND THE DEPTH OF FIELD 2 TO 5 TIMES. THIS PROJECT WILL TRANSFORM EXPERIMENTS BY INCREASING THE SPEED OF DATA CAPTURE, ENABLING INCREASED SAMPLE LABELING DENSITY, REDUCING THE SIZE OF DATASETS, REDUCING THE BURDEN ON DOWNSTREAM BIOINFORMATICS PIPELINES, AND EMPOWERING THE SPATIO-TEMPORAL STUDY OF OMICS PROCESSES IN LIVING CELLS WITH DECREASED PHOTOTOXICITY. THE EPSF OBJECTIVES WILL BE EASILY INTEGRATED INTO COMMERCIALLY AVAILABLE MICROSCOPES, ENHANCING ANY CLOSED-BOX IMAGING SYSTEM OR LAB-BUILT OPTICAL MICROSCOPE. RECENT RESEARCH HAS DEMONSTRATED THE NEED FOR NOVEL OPTICAL IMAGING APPROACHES IN SPATIAL OMICS APPLICATIONS, INCLUDING RATIOMETRIC IMAGING OF PROTEIN COMPLEXES, COUNTING OF MRNA IN GENE EXPRESSION, LOCALIZATION AND QUANTIFICATION OF GENOMIC LOCI, AND UNDERSTANDING OF CHROMATIN DYNAMICS. UNFORTUNATELY, CURRENT TECHNIQUES RELY ON HIGH RESOLUTION WIDEFIELD MICROSCOPES, DESIGNED TO PERFORM BEST AT FOCUS WITH LIMITED DEPTH OF FIELD, LEADING TO MISSED INFORMATION. THUS, CURRENT TECHNIQUES TURN TO AXIAL SCANNING TO CAPTURE THE ENTIRETY OF SAMPLE INFORMATION, RESULTING IN LONGER SAMPLE ACQUISITION TIMES, ADDITIONAL PHOTODAMAGE, BLOATED DATASETS, INCREASED DATA STORAGE, AND N-FOLD INCREASES IN COMPUTATION NEEDED IN BIOINFORMATICS PIPELINES. THE ABILITY TO CAPTURE MORE INFORMATION ABOUT A BIOLOGICAL SYSTEM UNDER INVESTIGATION IN A SINGLE IMAGE WITH EXTENDED DEPTH OF FIELD WILL ENHANCE SPATIAL OMICS STUDIES BY PROVIDING RESEARCHERS WITH MORE QUALITY INFORMATION IN LESS TIME, WITH LESS DATA TO PROCESS; HENCE, IT WILL IMPROVE THEIR UNDERSTANDING OF BIOLOGICAL SYSTEM STRUCTURE, FUNCTION, AND DYNAMICS. THIS WILL AID IN THE ADVANCEMENT OF SPATIAL GENOMICS, TRANSCRIPTOMICS, PROTEOMICS, AND EPIGENOMICS. THE EPSF OBJECTIVES PROPOSED HERE WILL ADDRESS BOTTLENECKS IN SPATIAL OMICS ASSAYS BY ACCELERATING CAPTURE OF QUALITY DATA, REPLACING THE NEED FOR COMPLEX AND TIME-CONSUMING MULTI-SLICE IMAGING. ADVANCES IN SPATIAL IMAGING WILL HELP ELUCIDATE MANY OUTSTANDING QUESTIONS IN BIOLOGICAL SYSTEMS. ULTIMATELY, THE EPSF OBJECTIVES WILL PROVIDE A COMMERCIALLY AVAILABLE HIGH-THROUGHPUT IMAGING TOOL THAT WILL GENERATE HIGH-QUALITY DATA FOR USE IN SPATIAL OMICS STUDIES, THUS CONTRIBUTING TO OUR KNOWLEDGE OF HUMAN DISEASE PROCESSES. DOUBLE HELIX OPTICS, A LEADER IN 3D IMAGING, WITH EXCLUSIVE LICENSING RIGHTS TO ITS LIGHT ENGINEERING TECHNOLOGY FROM U OF COLORADO AND STANFORD UNIVERSITY, IS OPTIMALLY POSITIONED TO SUCCESSFULLY BRING THIS PRODUCT TO MARKET.

LIGHT ENGINEERING MODULE FOR FAST HIGH-RESOLUTION WHOLE-CELL IMAGING

SBIR PHASE I: WIDEFIELD 3D SUPERRESOLUTION MICROSCOPY MODULE

SBIR PHASE I: THREE-DIMENSIONAL COMPUTATIONAL OPTICAL IMAGING SENSOR