Abstract: A multichannel imaging system generates an ensemble of images for each field of view of an object. Each image in the ensemble is intended to contain information from only one source among a plurality of sources for the object. However, due to crosstalk, at least a portion of the signal from a first source appears in a channel intended for a second source. Because the accuracy of the correction will be degraded if the images in an ensemble are spatially misaligned with respect to one another, the spatial offset between images is determined and a correction is applied to substantially eliminate the offset. Then, a correction to the signals is determined to substantially reduce the contributions to the signal in a channel from the signals in other channels. The signal processing can be employed to process the output signals for each of a plurality of different disclosed imaging systems.

Abstract: An illuminiation system for increasing a light signal from an object passing through a reflection cavity. The reflection cavity is disposed between spaced-apart, opposed first and second surfaces disposed on opposite sides of a moving stream of objects. A light collection system is disposed substantially orthogonal to a plane passing through the surfaces and the stream so as to collect light that is scattered from or emitted by the objects as they pass through a field of view disposed between the first and second surfaces. A beam of light from a laser source is directed through the stream of moving objects in a direction nearly orthogonal to the stream (but slightly inclined) and lying in the plane that extends through the surfaces and the stream. Due to the reflection angle and the distance between the stream and the first surface, the point at which the light reflected from the first surface intersects the stream on a second pass is displaced from where it passed though the stream on its initial pass.

Abstract: An illumination system for increasing a light signal from an object passing through a reflection cavity. The reflection cavity is disposed between spaced-apart, opposed first and second surfaces disposed on opposite sides of a moving stream of objects. A light collection system is disposed substantially orthogonal to a plane passing through the surfaces and the stream so as to collect light that is scattered from or emitted by the objects as they pass through a field of view disposed between the first and second surfaces. A beam of light from a laser source is directed through the stream of moving objects in a direction nearly orthogonal to the stream (but slightly inclined) and lying in the plane that extends through the surfaces and the stream. Due to the reflection angle and the distance between the stream and the first surface, the point at which the light reflected from the first surface intersects the stream on a second pass is displaced from where it passed though the stream on its initial pass.

Abstract: Light from an object such as a cell moving through an imaging system is collected and dispersed so that it can be imaged onto a time delay and integration (TDI) detector. The light can be emitted from a luminous object or can be light from a light source that has been scattered or not absorbed by the object or can include a light emission by one or more probes within or on the object. Multiple objects passing through the imaging system can be imaged, producing both scatter images and dispersed images at different locations on one or more TDI detectors.

Abstract: In an instrument generating images from the fluorescent emissions of a plurality of fluorescent dyes carried by objects in a flow stream, spectral dispersion is used to expand the images of the objects along one axis of a two-dimensional photosensor array according to emission wavelength. The dispersion is unable to completely separate the emissions of a plurality of dyes because the emission spectra of the dyes overlap in wavelength. The method of the present invention accomplishes accurate estimation of the intensity of the light received from each of a plurality of dyes by decomposing the two dimensional spectrally dispersed images into a set of characteristic parameters using either an iterative curve fitting optimization method or a linear algebraic method.

Abstract: Light from an object such as a cell moving through an imaging system is collected, and imaged onto a time delay integration (TDI) detector, producing a pixelated output signal in response to the image of the object. The light can be emitted from a luminous object, from a source and scattered by the object, or can be a fluorescent emission by one or more object probes. Light absorbed or reflected by the object can also produce images for determining specific characteristics of the object. In one set of embodiments, the movement of the object is synchronized with that of the pixelated output signal, which is controlled by the readout rate of the TDI detector. Alternatively, the readout rate of the pixelated output signal is not synchronized with the movement of the object, thereby permitting multiple signals to be produced for each of a plurality of objects over time.

Abstract: Light from an object such as a cell moving through an imaging system is collected and dispersed so that it is imaged onto a plurality of separate detectors. The light is spectrally dispersed by a plurality of spaced-apart dichroic reflectors, each detector receiving light from a different one of the dichroic reflectors. Each dichroic filter reflects light of a different predefined color, passing light of other colors. The output signal from each detector is indicative of a different characteristic of the object. In one configuration, each detector is provided with a separate imaging lens. In another configuration, the detectors are spaced at varying distances from the corresponding dichroic reflectors, so that separate imaging lenses are not required.

Abstract: When utilized in a flow imaging instrument, calibration beads provide a known data source that can be employed in various self-diagnostic, calibration and quality metric applications for the both the optical system of the flow imaging instrument, as well as the flow cell of the flow imaging instrument. Such data can be used to determine point spread functions associated with an imaging system, to determine a sensitivity of an imaging system, and to determine a focal point of the imaging system. Imagery collected from calibration beads can be used to determine core size and stability and TDI/flow speed synchronization. Calibration beads can be beneficially employed to enable stable system operation, even when very low sample concentration, or very small sample sizes are to be analyzed.

Abstract: An illumination system for increasing a light signal from an object passing through a reflection cavity. The reflection cavity is disposed between spaced-apart, opposed first and second surfaces disposed on opposite sides of a moving stream of objects. A light collection system is disposed substantially orthogonal to a plane passing through the surfaces and the stream so as to collect light that is scattered from or emitted by the objects as they pass through a field of view disposed between the first and second surfaces. A beam of light from a laser source is directed through the stream of moving objects in a direction nearly orthogonal to the stream (but slightly inclined) and lying in the plane that extends through the surfaces and the stream. Due to the reflection angle and the distance between the stream and the first surface, the point at which the light reflected from the first surface intersects the stream on a second pass is displaced from where it passed though the stream on its initial pass.

Abstract: Light from an object moving through an imaging system is collected, dispersed, and imaged onto a time delay integration (TDI) detector that is inclined relative to an axis of motion of the object, producing a pixilated output signal. In one embodiment, the movement of the image object over the TDI detector is asynchronous with the movement of the output signal producing an output signal that is a composite of the image of the object at varying focal point along the focal plane. In another embodiment, light from the object is periodically incident on the inclined TDI detector, producing a plurality of spaced apart images and corresponding output signals that propagate across the TDI detector. The inclined plane enables images of FISH probes or other components within an object to be produced at different focal points, so that the 3D spatial relationship between the FISH probes or components can be resolved.

Abstract: An illumination system for increasing a light signal from an object passing through a reflection cavity. The reflection cavity is disposed between spaced-apart, opposed first and second surfaces disposed on opposite sides of a moving stream of objects. A light collection system is disposed substantially orthogonal to a plane passing through the surfaces and the stream so as to collect light that is scattered from or emitted by the objects as they pass through a field of view disposed between the first and second surfaces. A beam of light from a laser source is directed through the stream of moving objects in a direction nearly orthogonal to the stream (but slightly inclined) and lying in the plane that extends through the surfaces and the stream. Due to the reflection angle and the distance between the stream and the first surface, the point at which the light reflected from the first surface intersects the stream on a second pass is displaced from where it passed though the stream on its initial pass.

Abstract: A multipass cavity system employs a beam of light that is reflected back and forth between reflective surfaces a plurality of times, illuminating a different portion of the field of view with each pass until the light exits the reflection cavity. The “recycling” of the light beam substantially improves the SNR of the detection system. The present invention is a beam alignment system for use in such a multipass cavity, correcting misalignment in four degrees of freedom; the horizontal and vertical axes, and angle in each of the vertical and horizontal axes. Angular or positional errors lateral to the direction of the beam can dramatically affect performance. The present invention enables the measurement and adjustment of each degree of freedom independently, in order to make beam steering corrections and maintain optical alignment. This is accomplished in an automated, closed-loop feedback control system.

Abstract: In automated computation-based interpretation of images, the accuracy and reliability of the detection and delineation of objects, known as “object segmentation,” is implemented so as to provide efficient performance. In a multi-step process, objects are first detected and captured into regions of interest (ROIs). Sets of pixels belonging to respective objects are then identified. Preferably object detection is achieved using both a two-dimensional (2D) low pass filter and a 2D edge enhancement filter. Two different gradient based edge enhancement filters are disclosed. One embodiment of the invention defines a (ROI) by first determining the center of objects by executing a plurality of decimations on the filtered image data, and then establishing object boundaries. In a second embodiment the ROI is defined by generating an amplitude histogram of the filtered image data, and for histograms exceeding a threshold determining by pixel which rows are to be included in the ROI.

Abstract: Frequency domain velocity measurements and time domain velocity measurements are made using light from cells or other objects. An optical grating is used to modulate the light from an object so that it has a frequency proportional to the velocity of the object. Depending upon the embodiment, the pitch of the optical grating is uniform or varying. The modulated light is detected and various signal processing techniques, such as a Fast Fourier Transform function, are used to indicate the velocity of the object. Preferably, the velocity measured is applied in determining a timing signal employed for synchronization of an image of the object and an detector signal in an optical analysis system that uses a time delay integration detector to determine characteristics of the object in response to light from the object.

Abstract: In an instrument generating images from the fluorescent emissions of a plurality of fluorescent dyes carried by objects in a flow stream, spectral dispersion is used to expand the images of the objects along one axis of a two-dimensional photosensor array according to emission wavelength. The dispersion is unable to completely separate the emissions of a plurality of dyes because the emission spectra of the dyes overlap in wavelength. The method of the present invention accomplishes accurate estimation of the intensity of the light received from each of a plurality of dyes by decomposing the two dimensional spectrally dispersed images into a set of characteristic parameters using either an iterative curve fitting optimization method or a linear algebraic method.

Abstract: A multichannel imaging system generates an ensemble of images for each field of view of an object. Each image in the ensemble is intended to contain information from only one source among a plurality of sources for the object. However, due to crosstalk, at least a portion of the signal from a first source appears in a channel intended for a second source. Because the accuracy of the correction will be degraded if the images in an ensemble are spatially misaligned with respect to one another, the spatial offset between images is determined and a correction is applied to substantially eliminate the offset. Then, a correction to the signals is determined to substantially reduce the contributions to the signal in a channel from the signals in other channels. The signal processing can be employed to process the output signals for each of a plurality of different disclosed imaging systems.

Abstract: Frequency domain velocity measurements and time domain velocity measurements are made using light from cells or other objects. An optical grating is used to modulate the light from an object so that it has a frequency proportional to the velocity of the object. Depending upon the embodiment, the pitch of the optical grating is uniform or varying. The modulated light is detected, producing an analog signal that is then digitally sampled. Time domain signal processing techniques are used to determine the velocity of the object from the digital samples. Preferably, the velocity measured is applied in determining a timing signal employed for synchronization of an image of the object and an detector signal in an optical analysis system that uses a time delay integration (TDI) detector to determine characteristics of the object in response to light from the object.

Abstract: Light from an object such as a cell moving through an imaging system is collected and dispersed so that it can be imaged onto a detector. The light can be emitted from a luminous object or can be light from a light source that has been scattered or not absorbed by the object or can include a light emission by one or more probes within or on the object. Multiple objects passing through the imaging system can be imaged, producing both scatter images and dispersed images at different locations on one or more detectors. In one embodiment, the detector is divided into a plurality of zones so that each of a plurality of different images are spectrally dispersed onto a different zone of the detector.

Abstract: A labeling method that labels an object or specific features of an object with labeled probes that provide a multiplexed signal that can be analyzed by spectral decomposition. This binary and higher encoding scheme can be employed to label components of biological cells. In each encoding scheme, labeled probes that selectively bind to a specific feature are required. The labeled probes include a binding element that binds to the feature, and at least one signaling component that generates a detectable signal, preferably a spectral signature. In one embodiment, adding multiple fluorescent dye molecules to each binding element provides the multiplexed signal. In another embodiment, adding only one signal compound to each binding element provides the multiplexed signal, such that some of the binding elements have a different signal compound added. The different signal compounds provide the multiplexed signal.

Abstract: Methods for constructing reporter labeled carriers (such as beads) using a plurality of optically distinguishable carriers for chemical synthesis or attachment, such that the number of unique reporters required to label a carrier is reduced. One embodiment employs carriers that themselves have optically distinguishing characteristics. A carrier's identity is encoded by the combination of the optical characteristics of its reporter set, as well as the optical characteristics of the carrier itself. In other embodiments, different reporters are discriminable based on the intensity of their color labels, their size, and/or other optically detectable characteristics, and not necessarily by the presence or absence of particular colors. Another embodiment is directed to generating a plurality of reporters from a plurality of singly labeled micro-particles. The present invention can be employed in conjunction with a split/add/pool (SAP) or a directed synthesis process.