Abstract: System, including methods and apparatus, for identifying and picking spectrally distinct colonies. In an exemplary method, a filter may be received in an optical path extending from a light source to a grayscale image detector. The filter may be configured to increase an intensity difference between a first type of colony and a spectrally distinct second type of colony. Colonies including both types may be received in the optical path. An image of the colonies may be obtained with the grayscale image detector. At least one of the types of colony may be identified in the image. One or more colonies of the at least one type may be picked robotically.

Abstract: A system and method to segment an image captured from an image capture device of a high content imaging system includes an image acquisition module that receives the image captured by the image capture device. A coarse object detection module develops a coarse segmented image, wherein each pixel of the coarse segmented image is associated with a corresponding pixel in the captured image and is identified as one of an object pixel and a background pixel. A marker identification module selects at least one marker pixel from the pixels of the coarse segmented image, wherein each marker pixel is one of a contiguous group of object pixels in the coarse segmented image that is furthest from a background pixel relative to neighboring pixels of the group.

Abstract: A method of generating in-focus images of measurement locations of a sample holder in a microscopy imaging system is provided. A camera array is positioned at a first distance from the sample holder. A first image of a measurement location is acquired using an imaging device disposed on the camera array. A candidate output image associated with the imaging device is developed in accordance with the first image. The camera array is positioned at a second distance from the sample holder and a second image of the measurement location is acquired using the imaging device. A portion of the candidate output image is updated in accordance with a portion of the second image in accordance with a selection criterion. The updated candidate image is transmitted.

Abstract: In a method for measuring luminescence of a biological sample utilizing two different luminescence reagents, the sample is agitated to improve mixing with the second luminescence reagent, allowing for a shorter delay time between injection of the second reagent and measurement of the resulting luminescence activity. The improved mixing may also allow for a shorter measurement time, thereby improving throughput when assaying a large number of samples.

Abstract: In an optical-based sample analysis, for example fluorescence-based or absorbance-based measurement, a selection is made between a first excitation light path and a second excitation light path. The first excitation light path directs excitation light from a light source, through an excitation monochromator, through an excitation filter, and to a sample. The second excitation light path directs excitation light from the light source, through the excitation filter, and to the sample while bypassing the excitation monochromator. Excitation light generated by the light source is transmitted along either the first excitation light path or the second excitation light path in accordance with the selection made, thereby irradiating the sample. In response the sample produces emission light (transmitted light in the case of absorbance measurements), which is transmitted to and measured by a light detector.

Abstract: In a method and system for identifying objects in an image, an image and training data are received. The training data identifies a pixel associated with an object of a particular type in the image. A plurality of filtered versions of the image are developed. The training data and the plurality of filtered versions of the image are processed to develop a trained model for classifying pixels associated with objects of the particular type. The trained model is applied to the image to identify pixels associated a plurality of objects of the particular type in the image. Additional image processing steps are developed to further refine the identified pixels for better fitting of the contour of the objects with their edges.

Abstract: An optical component for a microscope may include a low-autofluorescence substrate, or a substrate and a high-performance anti-reflective layer coating the substrate. An optical component may include a low-autofluorescence substrate and high-performance anti-reflective layer coating the low-autofluorescence substrate. The high-performance anti-reflective layer may be a low-autofluorescence high-performance anti-reflective layer. A microscope may include one or more such optical components.

Abstract: A system and method to segment an image captured from an image capture device of a high content imaging system includes an image acquisition module that receives the image captured by the image capture device. A coarse object detection module develops a coarse segmented image, wherein each pixel of the coarse segmented image is associated with a corresponding pixel in the captured image and is identified as one of an object pixel and a background pixel. A marker identification module selects at least one marker pixel from the pixels of the coarse segmented image, wherein each marker pixel is one of a contiguous group of object pixels in the coarse segmented image that is furthest from a background pixel relative to neighboring pixels of the group.

Abstract: Microscope system for, and methods of, imaging a sample including biological cells. In an exemplary method, light transmitted through the sample may be detected for a first set of focal positions to collect a first stack of images. Values of a focus metric may be calculated for the first stack of images. A candidate focal position may be determined based on the values. Photoluminescence may be detected from the sample for a second set of focal positions to collect a second stack of images. The second set of focal positions may define a smaller range than the first set of focal positions. At least one focal position of the second set of focal positions may be based on the candidate focal position. In other words, the candidate focal position may serve as a guide for finding a suitable photoluminescence focal position.

Abstract: A system and method for analyzing multi-dimensional images includes a high content imaging system that includes an image capture device. An image acquisition module receives a series of images of a biological sample captured by the image capture device, and the series of images includes a sequence of image planes. A human interface module receives from a user computer specifications of a first image analysis step and a second image analysis step. The first image analysis step specifies a first image processing operation that processes an image plane of a series of images in accordance with at least another image plane of the series of images and the second image analysis step specifies a second image processing operation that processes each image plane of a series of images independently of the other image planes of the series.

Abstract: A light detector includes a cooling device between a photomultiplier tube (PMT) device and a heat sink. A thermally conductive shield encloses the PMT device and the cooling device and is in thermal contact with the heat sink such that the heat sink transfers heat to the shield. The light detector may be included in sample analyzing apparatus configured for making optical measurements of a sample.

Abstract: A data acquisition system coupled to a mains power source and a method of operating the data acquisition system are disclosed. A test probe is configured to be coupled to a subject, and an analog to digital converter converts a signal from the test probe to samples. A noise replica generator generates estimates of noise in the samples, and a noise removal block removes from each sample an estimate of noise therein. When the subject is undergoing stimulation, the samples are provided to only the noise removal block. When the subject is not undergoing stimulation, the samples are provided to both the noise replica generator and the noise removal block.

Abstract: An apparatus for automatically conditioning a patch plate and a plenum of an electrophysiology measurement system is provided. An arm is linearly movable between a non-operative position and an operative position. An end effector mounted to one side of the arm is configured to condition the patch plate. Another end effector mounted to an opposite side of the arm is configured to condition the plenum. A linear actuator is coupled to the arm and is configured to drive movement of the arm between the operative position and the non-operative position. When the arm is positioned in the operative position, the arm is situated between the patch plate and the plenum.

Abstract: A system and method to segment an image captured from an image capture device of a high content imaging system includes an image acquisition module that receives the image captured by the image capture device. A coarse object detection module develops a coarse segmented image, wherein each pixel of the coarse segmented image is associated with a corresponding pixel in the captured image and is identified as one of an object pixel and a background pixel. A marker identification module selects at least one marker pixel from the pixels of the coarse segmented image, wherein each marker pixel is one of a contiguous group of object pixels in the coarse segmented image that is furthest from a background pixel relative to neighboring pixels of the group.

Abstract: System, including methods and apparatus, for sample processing. In exemplary embodiments, the system comprises a plurality of devices to perform a protocol on sample holders supporting samples, and also comprises a control system that coordinates operation of the plurality of devices, such that the protocol is performed automatically. Each device of at least two of the plurality of devices may have one or more status lights configured to display a plurality of different visual indicators each indicating a different status of the device. The at least two devices may utilize a same indicator scheme as one another for each different status indicated by the visual indicators. In some embodiments, the indicator scheme is user-configurable. In some embodiments, the one or more status lights of at least one device are provided by one or more recessed light-emitting strips.

Abstract: A computer-implemented method and system perform efficient and accurate fiber morphology analysis of fiber-containing biological samples. The images of objects comprising fiber and/or branching structure are obtained by camera and/or other imaging devices. Initial tracing seeds are obtained by variable modules. The adaptive threshold method is utilized for identifying tracing seeds candidates by local Principal Component Analysis (PCA) calculation and sorting out the seeds with low and high score. Each single fiber segment of interest is traced repeatedly utilizing PCA fitting calculation, and individual fiber segments are assembled by performing crossover matching calculation.

Abstract: An optical element holder includes receptacles for retaining optical elements, and is configured to move a selected optical element into an optical path whereby a light beam passes through the selected optical element. The optical element holder is configured to retain the optical elements in a manner that mitigates or avoids misalignment of the optical elements, thereby mitigating or avoiding unwanted deviations in the path of the light beam. The optical element holder may be part of a microscope or other optical instrument.

Abstract: A method of selecting a monoclonal cell colony that secretes a product of interest providing a plurality of cell culture spaces; each cell culture space has a respective assessment surface with a first binding agent immobilized on the assessment surface. The cells are incubated in a growth medium in the cell culture spaces for replication of the cells. At least some of the cells secrete a product of interest. A second binding agent is provided in the cell culture spaces. Initially, the second binding agent is not immobilized. Each of the first and second binding agents binds to the product of interest so that secretion of the product of interest by cells in any one of the cell culture spaces leads to a complex with the first binding agent, the product of interest and the second binding agent forming at the corresponding assessment surface of the cell culture space.

Abstract: Selected properties of a microplate comprising a plurality of sample wells are obtained by repetitively performing focusing functions to determine sequentially a well surface z-position and then a plate bottom z-position for a corresponding current x-y position based on an intensity indicative of a best focus of the well surface and the plate bottom respectively. The well surface z-position and the plate bottom z-position corresponding to each of the plurality of x-y positions are determined by repeating the steps of positioning the objective lens, performing the focusing function to determine the well surface z-position, and performing the focusing function for the plate bottom z-position. The well surface z-positions and the plate bottom z-positions at the plurality of x-y positions are used to generate data to determine the selected properties of the microplate.

Abstract: Systems and methods for measuring a target in a sample, the target being capable of generating an emitted light in response to an excitation light. In an example system, an excitation light source generates the excitation light along an excitation optical path. An attenuation filter arrangement selectively adds an attenuation filter to the excitation optical path. The attenuation filter attenuates the excitation light by a corresponding attenuation factor. The excitation light exits the attenuation filter arrangement along the excitation optical path to illuminate the sample. A light energy detector receives the emitted light generated in response to the excitation light, and outputs a measured signal level corresponding to an emitted light level. If the light energy detector indicates an overflow, signal measurement is repeated with attenuation filters of increasing attenuation factors until the measured signal level does not overflow.