University of Pittsburgh

Northwestern University

Northshore University Healthsystem

Yang Liu

Vadim Backman

Hemant Kumar Roy

Shikhar Uttam Fnu

Young L Kim

Jeremy D Rogers

Randall E Brand

Vladimir Turzhitsky

Hongqiang Ma

Hariharan Subramanian

Hoa V Pham

Prabhakar Pradhan

Pin Wang

Hoa Vinh Pham

Michael Siegel

Brand Randall

Michael Goldberg

Randall Brand

Ramesh Wali

A background correction method for a fluorescence microscopy system includes receiving a raw image stack, determining a number of temporal minimum intensity values for each pixel location from the raw image stack, and calculating an expected background value for each pixel location based on the number of temporal minimum intensity values for the pixel location. Also, an emitter localization method includes receiving a raw image stack, determining a rough position of each of a plurality of emitters within the raw image stack by employing a linear deconvolution process, and determining a precise position of each of the plurality of emitters by employing the rough position of the emitter and gradient fitting.

Systems and methods for robust background correction and/or emitter localization for super-resolution localization microscopy

Due to potential sampling errors (due to small tissue samples not necessarily directly from the developing tumor) and limited optical resolution (&#x2dc;1 micron), cancer may be missed or detected too late for optimal treatment, or conservative interpretation of indeterminate findings could lead to unnecessary surgery. The novel technology herein&#x2014;Spatial-domain Low-coherence Quantitative Phase Microscopy (SL-QPM)&#x2014;can detect structural alterations within cell nuclei with nanoscale sensitivity (0.9 nm) (or nuclear nano-morphology) for 'nano-pathological diagnosis' of cancer. SL-QPM uses original, unmodified cytology and histology specimens prepared with standard clinical protocols and stains. SL-QPM can easily integrate in existing clinical pathology laboratories. Results quantified the spatial distribution of optical path length or refractive index in individual nuclei with nanoscale sensitivity, which could be applied to studying nuclear nano-morphology as cancer progresses. The nuclear nano-morphology derived from SL-QPM offers significant diagnostic value in clinical care and subcellular mechanistic insights for basic and translational research.

Spatial-domain low-coherence quantitative phase microscopy

A method of estimating relative change of the 3D position of an object (e.g., sample drift in a microscopy system) having fiduciary markers that have an asymmetric joint point spread function distribution includes generating a plurality of calibration curves for each of the markers during a calibration phase including first calibration curves for a PSF width and second calibration curves for lateral bias. The method further includes capturing a first image of the markers during a data acquisition phase, generating a first joint 3D position for the markers using the first image, the first calibration curves and the second calibration curves, capturing a second image of the markers during the data acquisition phase, generating a second joint 3D position for the markers using the second image and the first and second calibration curves, and estimating the sample drift using the first joint 3D position and the second joint 3D position.

System and method for estimating and compensating for sample drift during data acquisition in fluorescence microscopy

Systems, methods and other embodiments associated with spatial-domain Low-coherence Quantitative Phase Microscopy (SL-QPM) are described herein. SL-QPM can detect structural alterations within cell nuclei with nanoscale sensitivity (0.9 nm) (or nuclear nano-morphology) for 'nano-pathological diagnosis' of cancer. SL-QPM uses original, unmodified cytology and histology specimens prepared with standard clinical protocols and stains. SL-QPM can easily integrate in existing clinical pathology laboratories. Results quantified the spatial distribution of optical path length or refractive index in individual nuclei with nanoscale sensitivity, which could be applied to studying nuclear nano-morphology as cancer progresses. The nuclear nano-morphology derived from SL-QPM offers significant diagnostic value in clinical care and subcellular mechanistic insights for basic and translational research. Techniques that provide for depth selective investigation of nuclear and other cellular features are disclosed.

Provided are systems, methods, and other embodiments associated with depth-resolved spatial-domain low-coherence quantitative phase microscopy for high-throughput analysis of 3D nanoscale architectural alterations in unstained tissue and cells. A spatial-domain low-coherence quantitative phase microscopy apparatus includes a drOPD mapping module, a transmission phase imaging module, and a bright-field and transmission phase imaging module. The drOPD mapping module includes a reflection-mode low-coherence spectral interferometry for drOPD mapping of unstained tissue. The transmission phase imaging module includes transmission quantitative phase imaging of unstained and stained tissue and produce an image registration reference. The bright-field and transmission phase imaging module includes bright-field imaging of H&E-stained tissue for nuclei identification and pathology correlation.

Depth-resolved spatial-domain low-coherence quantitative phase microscopy for unstained tissue and cells

Systems and methods that facilitate analysis of superficial tissue based at least in part on a depth-selective fiber optic probe are discussed herein. The depth-selective fiber optic probe can include an illumination fiber for providing light to the superficial tissue, a collection fiber for collected reflected light, a ball lens that couples the fibers, and a protective overtube that houses the ball lens and fibers. The distances between the ball lens and fibers and between the fibers can be optimized based on several factors, such as by minimizing the illumination spot size, maximizing the overlap between the illumination and collection spots, and based on the angle between the illumination and collection beams.

Depth-selective fiber-optic probe

Systems, methods, and apparatuses of elastic light scattering spectroscopy and low-coherence enhanced backscattering spectroscopy are described here. An apparatus couple-able to a light source and a target object, to facilitate light transmission between the light source and the target object, the apparatus comprises: a probe to emit incident light that is partially coherent obtained from the light source onto the target object and to receive interacted light, the interacted light to be backscattered light from illumination of the incident light on the target object, the probe comprising: a delivery channel having at least one delivery optical fiber with a distal end portion couple-able to the light source and a proximal end portion suited to couple the incident light to the target object, a collection channel having a first collection optical fiber suited to collect substantially co-polarized backscattered light and a second collection optical fiber suited to collect substantially cross-polarized backscattered light.

Systems, methods and apparatuses of elastic light scattering spectroscopy and low coherence enhanced backscattering spectroscopy

Systems and methods for identifying refractive-index fluctuations of a target are described in this application. One embodiment includes identifying one or more properties of emergent light, the emergent light to be emergent from a target, and determining refractive-index fluctuations of the target based on the one or more properties of the emergent light. The determining refractive-index fluctuations further comprises determining one or more of the variance of the refractive-index fluctuations and the spatial correlation length of the refractive-index fluctuations. The determining refractive-index fluctuations further comprises determining one or more of the variance of the refractive-index fluctuations and the spatial correlation length of the refractive-index fluctuations.

Method for identifying refractive-index fluctuations of a target

System for identifying refractive-index fluctuations of a target

Systems, methods, and apparatuses of low-coherence enhanced backscattering spectroscopy are described within this application. One embodiment includes providing incident light comprising at least one spectral component having low coherence, wherein the incident light is to be illuminated on a target object in vivo. An intensity of one or more of at least one spectral component and at least one angular component of backscattering angle of backscattered light is recorded, wherein the backscattered light is to be backscattered from illumination of the incident light on the target object and wherein the backscattering angle is an angle between incident light propagation direction and backscattered light propagation direction. The intensity of the at least one spectral component and the at least one backscattering angle of backscattered light is analyzed, to obtain one or more optical markers of the backscattered light, toward evaluating said properties.

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Sewickley, PA, United States of America

Yang Liu