Abstract: Methods for the image processing of cells are disclosed for the purpose of segmenting cell colonies for further processing to determine confluence, counting and morphology.

Abstract: Method and apparatus for displaying cultured cell wherein the image can be smoothly moved into and out of focus and can be zoomed in and out and panned.

Abstract: A method for pre-scanning a transparent cell culture plate with a plurality of wells to improve focus using a plurality of z-axis images and a method for focusing an optical system on a transparent cell culture plate by performing a Fourier transform on image data at different focus distance steps to reveal a pattern and using the pattern at each step to determine the focus distance.

Abstract: A method and apparatus for calibrating an imaging system provides a program stored in the imaging system having a graphical user interface and providing a plurality of tools to align hardware components of the imaging system including cameras for imaging cell culture vessels received by the imaging system and having a tool for providing a video image output of a cell culture vessel received in the imaging system.

Abstract: A plaque detection method and apparatus wherein at least one processor is programmed to receive above focus images to detect the presence of live cells without detecting the lysed cell materials, receive below focus images wherein virtual dark regions exist which are similar to cell shadows as seeds in a segmentation process and use contours around each resulting shape to obtain a subset that are more likely to be part of the cell population to define a cell map. A distance map is created in which each pixel value is the distance of that pixel from the nearest pixel of the cell map and the distance map is thresholded to create a first image of the places which are relatively far from the cells a second image with a smaller distance threshold to get an image that mimics the edges of the cells.

Abstract: A plaque detection method and apparatus wherein at least one processor is programmed to receive above focus images to detect the presence of live cells without detecting the lysed cell materials, receive below focus images wherein virtual dark regions exist which are similar to cell shadows as seeds in a segmentation process and use contours around each resulting shape to obtain a subset that are more likely to be part of the cell population to define a cell map. A distance map is created in which each pixel value is the distance of that pixel from the nearest pixel of the cell map and the distance map is thresholded to create a first image of the places which are relatively far from the cells a second image with a smaller distance threshold to get an image that mimics the edges of the cells.

Abstract: A cell culture incubator has an incubator cabinet with an internal chamber for the incubation of cells in one or more cell culture vessels and a door opening from an external environment to the internal chamber. At least two imagers configured for imaging the cells are within the internal chamber and a manipulator for manipulating the cells in the one or more cell culture vessels is within the internal chamber. A cell culture vessel transfer device moves the one or more cell culture vessels between the at least two imagers within the internal chamber and a controller is configured for controlling the cell culture transfer device to move cell culture vessels between the at least two imagers.

Abstract: In some aspects, the invention relates to selectively permeable cell culture vessel storage containers and their methods of use. In some embodiments, the containers comprise a gas-permeable membrane that is selectively impermeable to water vapor.

Abstract: A method and apparatus for measuring cells and cell confluence includes an imager for imaging a z-stack of bright field images and a processor for selecting a best focus bright field image at a z position of f microns in the z-stack of images. In the manner described herein, the processor selects a bright image n microns lower in the z-stack than the best focus bright field image and a dark image m microns higher in the stack than the best focus bright field image. The processor applies edge detection to the dark image to obtain an edge image and subtracts the edge image from the dark image and the processor applies an adaptive threshold to the bright image to create a mask and uses the adaptive thresholded image as seeds to evaluate the edge image to find cell candidates.

Abstract: Aspects of the present invention relate to a networked cell culture incubator and to methods for operating such an incubator. In one aspect, the cell culture incubator includes a network interface for communicating with a source of parameter data utilized successfully by other incubators. The incubator receives appropriate parameter data and conducts the incubation process as prescribed by the parameter data so as to provide an improved environment for cell culture growth. The incubator may share its own parameter data with the data source for use by other incubators. The incubator and data source may share other forms of data as well.

Abstract: A data collection hub and method wherein a controller is configured to receive data from a plurality of sensors sensing conditions related to the performance of operations on cells by at least one instrument. A database stores the data from the plurality of sensors and the controller is configured to compare data from the plurality of sensors for a past operation with the data for a more recent operation.

Abstract: Aspects relate to an automated cell culture incubator and to methods for using such an incubator. In one aspect, the cell culture incubator includes an incubator cabinet having a transfer chamber and an internal chamber that are arranged to form an airlock configuration. In some embodiments, objects placed into the incubator cabinet are sterilized using ozone produced by an ozone generator. The incubator may include one or more transfer devices that move objects between the transfer chamber and the internal chamber.

Abstract: A method and apparatus for searching cell images comprising storing cell images in an image database, generating index data for the stored images in the image database, wherein the index data includes image metadata and data extracted from the stored image data by analysis including morphological descriptors, applications of algorithms, machine learning and/or data mining.

Abstract: A cell incubator system comprising a housing having an internal chamber having a controlled temperature and gas mixture therein appropriate for the growth of particular cells for incubation of the particular cells in one or more cell culture vessels in the internal chamber and a plurality of cell operation stations in the internal chamber. The stations receive plates having wells for holding cells and wherein the cell operations stations perform operations on cells in the wells. The system has a robotic transport for moving plates from one station to another.

Abstract: Aspects relate to automated cell culture incubators comprising imaging systems, e.g., holographic or phase-contrast imagers, configured for imaging said cells within the incubators.

Abstract: A data collection hub and method wherein a controller is configured to receive data from a plurality of sensors sensing conditions related to the performance of operations on cells by at least one instrument. A database stores the data from the plurality of sensors and the controller is configured to compare data from the plurality of sensors for a past operation with the data for a more recent operation.

Abstract: A system for dissociating cells from a cell culture vessel. The system comprises an imaging system configured to image a plurality of cells in a cell culture vessel being dissociated from at least one surface of the cell culture vessel by at least one cell dissociation agent; and at least one controller coupled to the imaging system and configured to: control the imaging system to capture a sequence of images of at least some cells in the plurality of cells during dissociation; and identify when to neutralize the at least one cell dissociation agent using the sequence of images.

Abstract: A cell incubator system comprising a housing having an internal chamber having a controlled temperature and gas mixture therein appropriate for the growth of particular cells for incubation of the particular cells in one or more cell culture vessels in the internal chamber and a plurality of cell operation stations in the internal chamber. The stations receive plates having wells for holding cells and wherein the cell operations stations perform operations on cells in the wells. The system has a robotic transport for moving plates from one station to another.

Abstract: A method and system comprise taking a series of time spaced images of a cell culture having pathogens therein creating plaques, applying a stain to the cell culture, taking an image of the stained plaques, using the image of the stained culture to build a model of the plaques in earlier pre-stain images of the culture and displaying the pre-stain images and identifying the plaques therein based upon the model.

Abstract: Aspects of the invention relate to automated cell culture incubators. In some embodiments, automated cell culture incubators comprise an integrated manipulation device having one or more cell scrapers.