Abstract: Disclosed herein are multispectral detection methods and systems that can be used with image-forming optics configured to form an image of a sample. The systems include: (a) an imaging detector; (b) relay optics that include multiple optical elements, the relay optics positioned to relay the image formed by the image-forming optics to the imaging detector; (c) an actuator coupled to one of the optical elements in the relay optics and configured to adjust a position of the coupled optical element; and (d) control electronics configured to cause the actuator to adjust the position of the coupled optical element in the relay optics in response to a wavelength band selection by a wavelength selection element positioned to select one wavelength band for the image from among two or more wavelength bands within an overall wavelength range.

Abstract: A method including: providing a sample with M components to be labeled, where M>2; labeling the components with N stains, where N<M so that at least two components are labeled with a common stain; obtaining a set of spectral images of the sample; classifying different parts of the sample into respective classes that distinguish the commonly stained components based on the set of spectral images; and determining relative amounts of multiple ones of the M components in different regions of the sample. Related apparatus are also disclosed.

Abstract: Methods are disclosed for classifying different parts of a sample into respective classes based on an image stack that includes one or more images.

Abstract: Methods are disclosed that include: (a) applying a first stain to a first sample having a plurality of regions, where the first stain selectively binds to only a first subset of the regions of the first sample; (b) applying a second stain to the first sample, where the second stain binds to a second set of regions of the first sample; (c) obtaining an image of the first sample, and analyzing the image to obtain a first component image corresponding substantially only to spectral contributions from the first stain, and a second component image corresponding substantially only to spectral contributions from the second stain; and (d) training a classifier to identify regions of a second sample based on information derived from the first and second component images, the identified regions corresponding to the first subset of regions of the first sample.

Abstract: Disclosed herein are methods and apparatus for obtaining at least one absorption image and at least one birefringence image of a stained sample.

Abstract: Methods disclosed herein include: (a) determining positions of a plurality of cells based on one or more images of the cells; (b) for at least some of the plurality of cells, generating a matrix that includes two-dimensional information about positions of neighboring cells, and determining one or more numerical features based on the information in the matrix; and (c) classifying the at least some of the plurality of cells as belonging to at least one of multiple classes based on the numerical features.

Abstract: Disclosed are methods and systems for: (i) sequentially illuminating a specimen with different spatial distributions of light, wherein each illumination causes an object embedded in the specimen to emit radiation in response to the light; (ii) for each different spatial distribution of illumination light, imaging the radiation emitted from the specimen from each of multiple sides of the specimen; and (iii) determining information about the object in the specimen based on the imaged radiation from each of the multiple sides for each of the different spatial distributions of illumination light.

Abstract: A method of performing a Monte Carlo analysis uses a graphical processor unit of a computer system, individual data sets to be analyzed are allocated to respective pixel locations in a graphical processor unit memory for Monte Carlo simulation and the outcome of the Monte Carlo simulation is calculated for each data set using stream processing in the graphical processor unit.

Abstract: Apparatus and methods are disclosed for viewing low-birefringence structures within samples directly, with the eye, in real-time. The sample is placed between an entrance polarizer and analyzer polarizer, the transmission state of one of which is changed dynamically to create a modulated view of the scene; against this background, birefringent structures are visible because of their different appearance when modulated. Modulation rates of 4 or more states per second; use of 4 or more states, or even a continuum of states, which lie substantially on a latitude line on the Poincare sphere; and orientation of the polarization components to produce a uniform background; produce a clear view that does not produce operator fatigue. Broad-band wavelength operation spanning 50 nm or more, or the whole visible range, is achieved, and it is compatible with integration into other microscopy modes such as Hoffman relief contrast.

Abstract: The invention provides for surface mapping of in-vivo imaging subjects using a single camera and an illuminator that projects a plurality of targets such as spots on the subject. By limiting the depth-of-field of the camera lens, or of the illuminator optics, or both, a spatial plane is defined in which the spots are most sharply in focus. Controlled displacement of this plane relative to the subject is achieved through movement of the mechanical stage on which a subject is placed; or through movement of the best-focus plane by adjustment of the camera, lens, or illuminator optics. Images are taken at several relative positions of the best-focus plane and the subject, and the height of individual points on the subject is determined through analysis of focus, given the known displacements. A mesh or other surface can be constructed from individual point locations, to provide a surface map of the subject. Accuracy of 0.5 mm can be readily attained for mice and similarly sized subjects.

Abstract: An optical filter uses two or more reflective polarizers together with retarders to form birefringent filters with controlled transmission. The energy reflected by these polarizers is absorbed by one or more dichroic elements, which can be adjacent to a reflective polarizer; or spaced apart from it by one or more retarder elements. These dichroic elements act as dampers, so the energy of rays undergoing multiple reflections is markedly reduced or virtually eliminated, and high image quality is maintained. This provides a filter arrangement with enhanced spectral range, image quality, or greater extinction, or lower cost, compared to filters using dichroic or prism-type polarizers.

Abstract: Methods are disclosed for classifying different parts of a sample into respective classes based on an image stack that includes one or more images.

Abstract: Disclosed are methods and systems for: (i) positioning a specimen inside an optical measurement system according to a reference image of the specimen indicative of its position and orientation during an earlier measurement using the optical measurement system; and (ii) measuring radiation emitted from the positioned specimen to provide information about an object embedded in the specimen.

Abstract: The invention provides for surface mapping of in-vivo imaging subjects using a single camera and a moveable stage on which a subject animal for in-vivo imaging is placed. Images are taken and the stage is moved by known amounts along the optical axis, and the heights of individual features on the subject are determined through analysis of focus, given the known stage displacement. Alternatively, height of sub-regions of the subject are determined through analysis of focus. A mesh or other surface can be constructed from individual features, to provide a surface map of the subject. Accuracy of 0.5 mm or better can be attained for mice and similarly sized subjects.

Abstract: An optical filter assembly having selectable bandwidth is presented. The optical filter assembly includes a first optical filter, a first optical retarder with optical retardance R1, a second optical retarder with optical retardance R2, a polarization switch positioned between the first and second retarders which causes their retardances to substantially add in a first switch setting and to substantially subtract in a second switch setting, and an exit polarizer. A multispectral imaging system using tunable optical filters having selectable bandwidth is presented. A method of filtering light is also presented. The method includes providing a first optical filter, providing a dynamic bandwidth stage including a polarization switch, selecting a first setting of the polarization switch, and producing a first filter action for light passing through the first filter and the dynamic bandwidth stage.

Abstract: Methods are disclosed for classifying different parts of a sample into respective classes based on an image stack that includes one or more images.

Abstract: Apparatus and methods are disclosed for viewing low-birefringence structures within samples directly, with the eye, in real-time. The sample is placed between an entrance polarizer and analyzer polarizer, the transmission state of one of which is changed dynamically to create a modulated view of the scene; against this background, birefringent structures are visible because of their different appearance when modulated. Modulation rates of 4 or more states per second; use of 4 or more states, or even a continuum of states, which lie substantially on a latitude line on the Poincare sphere; and orientation of the polarization components to produce a uniform background; produce a clear view that does not produce operator fatigue. Broad-band wavelength operation spanning 50 nm or more, or the whole visible range, is achieved, and it is compatible with integration into other microscopy modes such as Hoffman relief contrast.

Abstract: An athermalized birefringent filter for shifts in center wavelength and in bandwidth incorporates fixed retarder elements such as quartz or film retarders, along with electrically-variable retarder elements such as liquid crystal variable retarder cells. A control mechanism determines the amount of thermal drift in the fixed retarder element and produces an equal change in the variable retarder element. The sign of the change depends on whether the variable retarder element adds its retardance with that of the fixed retarder element, or opposes it. This change compensates for the thermal drift of the fixed retarder element. Further, the variable retarder element is constructed to provide the necessary range of retardance adjustment for spectral tuning and thermal compensation over a target thermal range. The control mechanism ensures that, for any specified wavelength, the birefringent filter operates in the same order over the full target thermal range.

Abstract: The invention features a method including: (i) providing spectrally resolved information about light coming from different spatial locations in a sample comprising deep tissue in response to an illumination of the sample, wherein the light includes contributions from different components in the sample; (ii) decomposing the spectrally resolved information for each of at least some of the different spatial locations into contributions from spectral estimates associated with at least some of the components in the sample; and (iii) constructing a deep tissue image of the sample based on the decomposition to preferentially show a selected one of the components.

Abstract: An optical filter assembly having selectable bandwidth is presented. The optical filter assembly includes a first optical filter, a first optical retarder with optical retardance R1, a second optical retarder with optical retardance R2, a polarization switch positioned between the first and second retarders which causes their retardances to substantially add in a first switch setting and to substantially subtract in a second switch setting, and an exit polarizer. A multispectral imaging system using tunable optical filters having selectable bandwidth is presented. A method of filtering light is also presented. The method includes providing a first optical filter, providing a dynamic bandwidth stage including a polarization switch, selecting a first setting of the polarization switch, and producing a first filter action for light passing through the first filter and the dynamic bandwidth stage.