Abstract: Automated methods and devices that facilitate iterative staining of biological samples from imaging applications are provided. The methods include the steps of providing a small volume flow cell containing a biological sample, applying a stain to the biological sample, combining at least two precursor reagents to form an activated destaining agent and wherein the activated destaining agent decomposition rate is greater than or similar to the destaining reaction rate, flowing the destaining agent over the biological sample at a flow rate that is greater than the decomposition rate of the activated destaining agent, and releasing the sample from the flow cell wherein the integrity of the sample is intact. The process of staining, combining and flowing may be iteratively repeated.

Abstract: A method of autofocusing includes capturing first, second and third images of a sample, at respective first, second and third sample distances and respective first, second and third lateral positions determined with respect to an objective; determining a quantitative characteristic for the first, second and third images; determining a primary sample distance based upon at least the quantitative characteristics for the first, second, and third images; and capturing a primary image of the sample at the primary sample distance and at a primary lateral position that is offset from the first, second and third lateral positions.

Abstract: Imaging systems and methods for generating images of a sample wherein the system comprises an illumination source for illuminating the sample; an image viewing subsystem for capturing images from the sample; one or more liquid crystal panels and one or more birefringent elements, which are positioned between the sample and the image viewing subsystem, so that the images from the sample pass through the liquid crystal panels and the birefringent elements before reaching the image viewing subsystem; a device that changes one or more polarization states of the liquid crystal panels; and a controller that is configured to cause the device to change the polarization states of the liquid crystal panels.

Abstract: The invention provides method for locating one or more substantially circular-shaped tissue sample positioned on a solid support. The method involves the steps of transmitting light of a preselected wavelength onto a tissue sample, wherein the light induces the tissue sample to autofluoresce, identifying the center location of the tissue sample using the autofluoresced light, correlating the coordinates of the center location of the tissue sample on the solid support using an x, y-coordinate system, and mapping the coordinates of the tissue sample on the solid support to differentiate tissue sample containing regions from blank regions on the solid support. In a second aspect, the invention provides an apparatus for locating one or more substantially circular-shaped tissue sample positioned on a solid support.

Abstract: A system for analyzing tissue samples, that generally comprises, a storage device for at least temporarily storing one or more images of one or more cells, wherein the images comprise a plurality of channels; and a processor that is adapted to determine the extent to which a biomarker may have translocated from at least one subcellular region to another subcellular region; and then to generate a score corresponding to the extent of translocation.

Abstract: A method for the imaging of protein expression and location in biological samples using optical segmentation is provided. The steps comprise acquiring a fluorescent image of a biological sample, analyzing the image and generating a masking pattern corresponding to a specific structure within the biological sample, transforming the masking pattern into the spatial coordinates of a digital micro-mirror device (DMD) which may then be projected onto the biological sample and obtaining a masked fluorescent image. Also provided is an image analysis system for imaging of protein expression and location in biological samples using optical segmentation.

Abstract: The present disclosure concerns a method and system for assessing image quality of sub-images used to form a composite image using an algorithm developed by applying statistical correlation techniques to historical data on features of sub-images which were manually evaluated by experts and using those assessment to make decisions about the further processing of the sub-images which are being assessed. The method and system find particular value in the processing of sub-images generated while there is relative motion between the specimen under examination and the objective lens of a microscope such as when the microscope stage follows a planned traverse in the focal plane and a digital image is created at intervals correlated to the motion of the stage so that a region of interest in the specimen under examination is covered by the sub-images.

Abstract: Methods and systems for digitally enhancing an initial image of a material to which a plurality of stains were previously applied, that generally comprise: unmixing the image into a plurality of individual reconstructed images, each individual image corresponding to one of the stains; estimating a residual image corresponding to the difference between the original image and the reconstructed images; adjusting one or more components of the individual images; mixing the adjusted components using one or more estimated mixing coefficients; and adding the residual image to the mixed adjusted components to generate an enhanced image.

Abstract: The invention provides method for locating one or more substantially circular-shaped tissue sample positioned on a solid support. The method involves the steps of transmitting light of a preselected wavelength onto a tissue sample, wherein the light induces the tissue sample to autofluoresce, identifying the center location of the tissue sample using the autofluoresced light, correlating the coordinates of the center location of the tissue sample on the solid support using an x, y-coordinate system, and mapping the coordinates of the tissue sample on the solid support to differentiate tissue sample containing regions from blank regions on the solid support. In a second aspect, the invention provides an apparatus for locating one or more substantially circular-shaped tissue sample positioned on a solid support.

Abstract: Methods for probing multiple targets in a biological sample are provided. The methods include the steps of providing a biological sample containing multiple targets, binding at least one fluorescent probe to one or more target present in the sample, and binding at least at least one control probe to one or more target present in the sample. The methods include the steps of observing a signal from the fluorescent probe and a control signal from the control probe and applying to the sample a basic solution containing an oxidizing agent that selectively inactivates the fluorescent probe and not the control probe. The methods further include the steps of binding at least one fluorescent probe to one or more target present in the sample and observing a signal from the fluorescent probe. The methods disclosed herein also provide for multiple iterations of binding, observing, and oxidizing for deriving information about multiple targets in a single sample. An associated kit is also provided.

Abstract: Methods for detecting multiple targets in a biological sample are provided. The methods includes contacting the sample with a first probe; physically binding the first probe to a first target; observing a first signal from the first probe; applying a chemical agent to modify the first signal; contacting the sample with a second probe; physically binding the second probe to a second target; and observing a second signal from the second probe. The methods disclosed herein also provide for multiple iterations of binding, observing, signal modification for deriving information about multiple targets in a single sample. An associated kit and device are also provided.

Abstract: Methods for detecting multiple targets in a biological sample are provided. The methods includes contacting the sample with a first probe; physically binding the first probe to a first target; observing a first signal from the first probe; applying a chemical agent to modify the first signal; contacting the sample with a second probe; physically binding the second probe to a second target; and observing a second signal from the second probe. The methods disclosed herein also provide for multiple iterations of binding, observing, signal modification for deriving information about multiple targets in a single sample. An associated kit and device are also provided.

Abstract: A system and method for optical transmission of ultrasound data signals from a probe to an image processing system is provided. By using a silicon-based optical modulator to encode ultrasound data signals onto an optical signal, an optical transmission link between the ultrasound probe and the image processing system can achieve a high signal to noise ratio with a lower power input.

Abstract: Automated methods and devices that facilitate iterative staining of biological samples from imaging applications are provided. The methods include the steps of providing a small volume flow cell containing a biological sample, applying a stain to the biological sample, combining at least two precursor reagents to form an activated destaining agent and wherein the activated destaining agent decomposition rate is greater than or similar to the destaining reaction rate, and flowing the destaining agent over the biological sample at a flow rate that is greater than the decomposition rate of the activated destaining agent. The process of staining, combining and flowing may be iteratively repeated. Also disclosed herein are devices for iterative staining of biological samples comprising a flow cell, in fluid communication with a premixer, wherein the volume capacity of the premixer is smaller than about five times the volume capacity of the flow cell.

Abstract: A digital optical microscope includes a primary image sensor that generates a primary image of a sample at a primary frame rate, an auxiliary image sensor that generates an auxiliary image of the sample at an auxiliary frame rate that is faster than the primary frame rate, and a controller that adjusts a focal distance between an objective lens and the sample along an optical axis in response to the auxiliary image, thereby autofocusing the primary image on the sample. The primary image sensor generates the primary image in response to the autofocusing.

Abstract: A digital optical microscope includes a primary image sensor that generates a primary image of a sample at a primary frame rate, an auxiliary image sensor that generates an auxiliary image of the sample at an auxiliary frame rate that is faster than the primary frame rate, and a controller that adjusts a focal distance between an objective lens and the sample along an optical axis in response to the auxiliary image, thereby autofocusing the primary image on the sample. The primary image sensor generates the primary image in response to the autofocusing.

Abstract: A method of autofocusing includes capturing first, second and third images of a sample, at respective first, second and third sample distances and respective first, second and third lateral positions determined with respect to an objective; determining a quantitative characteristic for the first, second and third images; determining a primary sample distance based upon at least the quantitative characteristics for the first, second, and third images; and capturing a primary image of the sample at the primary sample distance and at a primary lateral position that is offset from the first, second and third lateral positions.

Abstract: Embodiments of methods, apparatuses, devices, and/or systems for a tunable laser are described. An apparatus includes: a tunable laser cavity including at least three mirrors, at least one filter and a plurality of crystals, wherein the three mirrors are substantially arranged in a lambda configuration, the filter includes a birefringent filter and an etalon, at least one of the crystals comprises a Cologuiriite crystal, and at least one other of the crystals comprises a nonlinear crystal, wherein the mirrors, the filter, and the plurality are configured for providing electromagnetic radiation of an approximately single frequency; and at least one electromagnetic radiation source being coupled to the laser cavity, wherein the electromagnetic radiation source is capable of providing electromagnetic radiation having an approximately particular wavelength to the laser cavity.

Abstract: An optical imaging apparatus comprising an aspheric objective configured to receive optical radiation from an object and an optical sensing device. The aspheric objective comprises a first reflective aspheric mirror and a second reflective aspheric mirror optically coupled to the first reflective aspheric mirror such that optical radiation received from the object is reflected by the first reflective aspheric mirror to the second reflective aspheric mirror. The optical sensing device disposed adjacent to a non-reflective side of the first aspheric mirror and configured to render digitized images of reflected optical radiation representative of the object.

Abstract: Methods for detecting multiple targets in a biological sample are provided. The methods includes contacting the sample with a first probe; physically binding the first probe to a first target; observing a first signal from the first probe; applying a chemical agent to modify the first signal; contacting the sample with a second probe; physically binding the second probe to a second target; and observing a second signal from the second probe. The methods disclosed herein also provide for multiple iterations of binding, observing, signal modification for deriving information about multiple targets in a single sample. An associated kit and device are also provided.