Abstract: An imaging system is configured with an autofocus operation that refocuses multiple cameras of the imaging system on detected features of interest, instead of on the whole image of the sample. Focus measures are calculated on the detected features, and then aggregated to focus distances of actuator moving the camera array, the sample stage, or individual cameras based on a maximization of detected features to be in focus. After the refocus, the imaging system recaptures new images and analyzes features on the new images to generate statistical characterization of the sample based on the classification of the features.

Abstract: An imaging system having multiple cameras providing a large field of view with sufficient resolution can be used for tracking movements of cells from their positions in a tissue sample into multiple isolated areas such as into individual microwells in a well plate. By determining the beginning and the end of the movements of each cell, the imaging system can associate the microwell locations to the original cell positions in the sample. Together with an analysis of the cells in the microwells, either individually or together with barcode beads, the analysis can achieve the spatial information needed for constructing a map of the molecular information with respect to the positions of the cells in the sample.

Abstract: A system can be used for imaging volumetric samples using a camera array to capture images under different illumination patterns at different axial planes of focus, and at optionally varying lateral fields of view. The sequence of images taken under the different illumination patterns and optional varying lateral fields of view can be processed to generate an image representation of the sample at a focus plane of the sample. Multiple image representations at different focus planes are assembled to form a 3D volumetric representation of the sample.

Abstract: A system and method for high resolution multi-fluorescence imaging with synchronized image acquisition amongst sensors can be used to simultaneously capture fluorescence signals from multiple fluorophores over extremely large fields of view. The system can include an array of micro-cameras, along with a particular arrangement of fluorescent filters that can be fixed in one location or moved to new locations.

Abstract: A microscopy includes multiple cameras working together to capture image data of a sample having a group of organisms distributed over a wide area, under the influence of an excitation instrument. A first processor is coupled to each camera to process the image data captured by the camera. Outputs from the multiple first processors are aggregated and streamed serially to a second processor for tracking the organisms. The presence of the multiple cameras capturing images from the sample, configured with 50% or more overlap, can allow 3D tracking of the organisms through photogrammetry.

Abstract: A system and method for high resolution multi-fluorescence imaging with synchronized image acquisition amongst sensors can be used to simultaneously capture fluorescence signals from multiple fluorophores over extremely large fields of view. The system can include an array of micro-cameras, along with a particular arrangement of fluorescent filters that can be fixed in one location or moved to new locations.

Abstract: A method to capture microscopy images from multiple image sensors and to relay them to one or more central processing units while minimizing delay in image capture can include the co-optimization of image acquisition hardware, data aggregation digital logic, firmware, and integration with data post processing on the central processing units. The methods can include organizing the incoming image data into data packets containing partial image frames, together with configuring the central processing units to be capable of analyzing the received partial image frames. The quick analysis of the images, e.g., on the partial image frames, can allow the computational system to rapidly respond to the captured images, such as to provide feed back on the captured images before the next images are to be captured.

Abstract: A method to capture microscopy images from multiple image sensors and to relay them to one or more central processing units while minimizing delay in image capture can include the co-optimization of image acquisition hardware, data aggregation digital logic, firmware, and integration with data post processing on the central processing units. The methods can include organizing the incoming image data into data packets containing partial image frames, together with configuring the central processing units to be capable of analyzing the received partial image frames. The quick analysis of the images, e.g., on the partial image frames, can allow the computational system to rapidly respond to the captured images, such as to provide feed back on the captured images before the next images are to be captured.

Abstract: A system and method for high-resolution polarimetric imaging can include an array of micro-cameras to simultaneously capture polarized optical information from a wide area. Polarized illumination sources can be placed below and/or above the sample to direct polarized light to the sample during image capture. Post processing can be performed on the captured images to obtain polarimetric properties of the sample.

Abstract: An imaging system is configured with an autofocus operation that refocuses multiple cameras of the imaging system on detected features of interest, instead of on the whole image of the sample. Focus measures are calculated on the detected features, and then aggregated to focus distances of actuator moving the camera array, the sample stage, or individual cameras based on a maximization of detected features to be in focus. After the refocus, the imaging system recaptures new images and analyzes features on the new images to generate statistical characterization of the sample based on the classification of the features.

Abstract: A method to capture microscopy images from multiple image sensors and to relay them to one or more central processing units with high frame rates can include preprocessing the image data from the image sensors to reduce the sizes of the captured images, before sending the image data to a central processing station for analysis. Using multiple image sensors and an image reduction process, large image frames of over 20 megapixels and up to 1 gigapixel or more can be obtained at high imaging frame rates of 30 or more to up to hundreds or thousands of frames per second.