Abstract: A classification training method for training classifiers adapted to identify specific mutations associated with different cancer including identifying driver mutations. First cells from mutation cell lines derived from conditions having the number of driver mutations are acquired and 3D image feature data from the number of first cells is identified. 3D cell imaging data from the number of first cells and from other malignant cells is generated, where cell imaging data includes a number of first individual cell images. A second set of 3D cell imaging data is generated from a set of normal cells where the number of driver mutations are expected to occur, where the second set of cell imaging data includes second individual cell images. Supervised learning is conducted based on cell line status as ground truth to generate a classifier.

Abstract: A method of treating a malignancy in a human subject by analyzing pseudo-projection images of cells obtained from a sputum specimen obtained from a subject employs a biological specimen classifier that identifies cells from the sputum specimen as normal or abnormal. If abnormal cells are detected, then the abnormal cells are further classified as dysplastic or cancerous. If the cells are classified as dysplastic, then an immunomodulating agent is administered to the subject over a predetermined time period designed to achieve a therapeutic dosage.

Abstract: A method for 3D imaging of a biologic object (1) in an optical tomography system where a subcellular structure of a biological object (1) is labeled by introducing at least one nanoparticle-biomarker. The labeled biological object (1) is moved relatively to a microscope objective (62) to present varying angles of view and the labeled biological object (1) is illuminated with radiation having wavelengths between 150 nm and 900 nm. Radiation transmitted through the labeled biological object (1) and the microscope objective (62) within at least one wavelength bands is sensed with a color camera, or with a set of at least four monochrome cameras. A plurality of cross-sectional images of the biological object (1) from the sensed radiation is formed and reconstructed to make a 3D image of the labeled biological object (1).

Abstract: A method for 3D imaging of cells in an optical tomography system includes moving a biological object relatively to a microscope objective to present varying angles of view. The biological object is illuminated with radiation having a spectral bandwidth limited to wavelengths between 150 nm and 390 nm. Radiation transmitted through the biological object and the microscope objective is sensed with a camera from a plurality of differing view angles. A plurality of pseudoprojections of the biological object from the sensed radiation is formed and the plurality of pseudoprojections is reconstructed to form a 3D image of the cell.

Abstract: An object of interest is illuminated within the field of view of a microscope objective lens located to receive light passing through the object of interest. Light transmitted through the microscope objective lens impinges upon a variable power element. The variable power element is driven with respect to the microscope objective lens to scan through multiple focal planes in the object of interest. Light transmitted from the variable power element is sensed by a sensing element or array.

Abstract: A system and method for detecting poor quality images in an optical tomography system includes an acquisition apparatus for acquiring a set of pseudo-projection images of an object having a center of mass, where each of the set of pseudo-projection images is acquired at a different angle of view. A reconstruction apparatus is coupled to receive the pseudo-projection images, for reconstruction of the pseudo-projection images into 3D reconstruction images. A quality apparatus is coupled to receive the 3D reconstruction images and operates to detect of selected features that characterize poor quality reconstructions.

Abstract: A method for 3D imaging of cells in an optical tomography system includes moving a biological object relatively to a microscope objective to present varying angles of view. The biological object is illuminated with radiation having a spectral bandwidth limited to wavelengths between 150 nm and 390 nm. Radiation transmitted through the biological object and the microscope objective is sensed with a camera from a plurality of differing view angles. A plurality of pseudoprojections of the biological object from the sensed radiation is formed and the plurality of pseudoprojections is reconstructed to form a 3D image of the cell.

Abstract: Correcting pattern noise projection images includes acquiring a set of projection images with an optical tomography system including a processor, where each of the set of projection images is acquired at a different angle of view. A threshold is applied to each projection image produce a set of threshold images. Each threshold image may optionally be dilated to produce a set of dilated images that are summed to form an ensemble image. Each of the dilated images is processed to produce a set of binary images. The set of binary images are summed to form an ensemble mask. The ensemble image is divided by the ensemble mask to yield a background pattern noise image. Each projection image is multiplied by a scaling factor and divided by the background pattern noise to produce a quotient image that is filtered to produce a noise corrected projection image.

Abstract: An optical tomography system for imaging an object of interest including a light source for illuminating the object of interest with a plurality of radiation beams. The object of interest is held within an object containing tube such that it is illuminated by the plurality of radiation beams to produce emerging radiation from the object containing tube, a detector array is located to receive the emerging radiation and produce imaging data used by a mechanism for tracking the object of interest.

Abstract: A method for loading a sample for imaging by an optical tomography system. A sample volume including at least one microscopic sample and a viscous fluid is coaxially loaded into a sample delivery tube. The sample volume is impelled through a focus cell into a capillary tube, where the capillary tube has a smaller crossectional area than the sample delivery tube, so that a reduced volume of the at least one microscopic sample and viscous fluid is constrained to a central region within the capillary tube.

Abstract: A method for reconstructing three-dimensional (3D) tomographic images. A set of pseudo-projection images of an object is acquired. Error corrections are applied to the set of pseudo-projection images to produce a set of corrected pseudo-projection images. The set of corrected pseudo-projection images are processed to produce (3D) tomographic images.

Abstract: A scanning method for scanning samples of biological cells using optical tomography includes preparing, acquiring, reconstructing and viewing three-dimensional images of cell samples. Concentration and enrichment of the cell sample follows. The cell sample is stained. Cells are isolated from the cell sample and purified. A cell/solvent mixture is injected into a gel by centrifugation. A cell/gel mixture is injected into a capillary tube until a cell appears centered in a field of view using a stopped-flow method. An optical imaging system, such as a fixed or variable motion optical tomography system acquires a projection image. The sample is rotated about a tube axis to generate additional projections. Once image acquisition is completed, the acquired image projections are corrected for errors. A computer or other equivalent processor is used to compute filtered backprojection information for 3D reconstruction.

Abstract: An optical projection tomography system is illuminated with a light source. An object-containing tube, a portion of which is located within the region illuminated by the light source, contains an object of interest that has a feature of interest. A detector is located to receive emerging radiation from the object of interest. A lens, including optical field extension elements, is located in the optical path between the object region and the detector, such that light rays from multiple object planes in the object-containing tube simultaneously focus on the detector. The object-containing tube moves relatively to the detector and the lens operate to provide multiple views of the object region for producing an image of the feature of interest at each view.

Abstract: A system for optical imaging of a thick specimen that permits rapid acquisition of data necessary for tomographic reconstruction of the three-dimensional (3D) image. One method involves the scanning of the focal plane of an imaging system and integrating the range of focal planes onto a detector. The focal plane of an optical imaging system is scanned along the axis perpendicular to said plane through the thickness of a specimen during a single detector exposure. Secondly, methods for reducing light scatter when using illumination point sources are presented. Both approaches yield shadowgrams. This process is repeated from multiple perspectives, either in series using a single illumination/detection subsystem, or in parallel using several illumination/detection subsystems. A set of pseudo-projections is generated, which are input to a three dimensional tomographic image reconstruction algorithm.

Abstract: An apparatus and method for sorting particles in a laminar flow microfluidic channel includes a cantilevered coaxial flow injector in a microfluidic device, the cantilevered coaxial flow injector including an elongated cantilever element integrated into the microfluidic device. A coaxial channel runs through the elongated cantilever element, where coaxial channel is sized to pass particles of a predetermined size. An actuator is coupled to the elongated cantilever element, for actuating said elongated cantilever element.

Abstract: An apparatus and method for correction of relative object-detector motion between successive views during optical tomographic imaging in three dimensions. An object of interest is illuminated to produce an image. A lateral offset correction value is determined for the image. An axial offset correction value is determined for the image. The lateral offset correction value and the axial offset correction value are applied to the image to produce a corrected file image.

Abstract: A method for automated cell enrichment preparation where biological cells are injected into a first subchamber and flowed through the first subchamber, through a large pore filter and into a second subchamber so that the large pore filter retains particles large particles in the first subchamber, while the biological cells pass through the first filter into the second subchamber and are retained by a small pore filter. After clearing, the biological cells are stained. A solvent exchange leaves the biological cells in solvent and they are released into a concentration module where a portion of the solvent is removed to form an enriched concentrated cell suspension.

Abstract: Motion correction for optical tomographic imaging in three dimensions. An object of interest is illuminated to produce an image. A lateral offset correction value is determined for the image. An axial offset correction value is determined for the image. The lateral offset correction value and the axial offset correction value are applied to the image to produce a corrected file image.

Abstract: Motion of an object of interest, such as a cell, has a variable velocity that can be varied on a cell-by-cell basis. Cell velocity is controlled in one example by packing cells into a capillary tube, or any other linear substrate that provides optically equivalent 360 degree viewing access, so that the cells are stationary within the capillary tube, but the capillary tube is translated and rotated mechanically through a variable motion optical tomography reconstruction cylinder. The capillary tube motion may advantageously be controlled in a start-and-stop fashion and translated and rotated at any velocity for any motion interval, under the control of a computer program. As such, there are several configurations of the optical tomography system that take advantage of this controlled motion capability. Additionally, the use of polarization filters and phase plates to reduce light scatter and diffraction background noise is described.

Abstract: A parallel-beam optical tomography system for imaging an object of interest includes a parallel ray beam radiation source that illuminates the object of interest with a plurality of parallel radiation beams. After passing through the object of interest the pattern of transmitted or emitted radiation intensities is magnified by a post specimen optical element or elements. An object containing tube is located within an outer tube, wherein the object of interest is held within or flows through the object containing tube. A motor may be coupled to rotate and/or translate the object containing tube to present differing views of the object of interest. One or more detector arrays are located to receive the emerging radiation from the post specimen magnifying optic. Two- or three-dimensional images may be reconstructed from the magnified parallel projection data.