Abstract: Systems and methods for capturing a digital image of a slide using an imaging line sensor and a focusing line sensor. In an embodiment, a beam-splitter is optically coupled to an objective lens and configured to receive one or more images of a portion of a sample through the objective lens. The beam-splitter simultaneously provides a first portion of the one or more images to the focusing sensor and a second portion of the one or more images to the imaging sensor. A processor controls the stage and/or objective lens such that each portion of the one or more images is received by the focusing sensor prior to it being received by the imaging sensor. In this manner, a focus of the objective lens can be controlled using data received from the focusing sensor prior to capturing an image of a portion of the sample using the imaging sensor.

Abstract: Automatic nuclear segmentation. In an embodiment, a plurality of superpixels are determined in a digital image. For each of the superpixels, any superpixels located within a search radius from the superpixel are identified, and, for each unique local combination between the superpixel and any identified superpixels located within the search radius from the superpixel, a local score for the local combination is determined. One of a plurality of global sets of local combinations with an optimum global score is identified based on the determined local scores.

Abstract: Systems and methods are provided to facilitate consultations between a referral source (e.g., labs, pathologists and patients) and a consultant (e.g., pathologist, radiologist, or other digital image analyst). Links between the various referral sources and consultants are established through a scanning center via a data communication network such as the Internet. The referral source sends a slide to the scanning center where the corresponding digital slide is posted for review and analysis by the consultant. Upon completion of the analysis and report, a digital slide conference is conducted through the scanning center that provides a venue for direct communication regarding the consultation. The scanning center may also facilitate payment from the referral source to the consultant.

Abstract: Microscope slide scanner. In an embodiment the microscope slide scanner comprises a single enclosure unit that includes at least one objective lens, at least one line scan camera, at least one communication port, and at least one processor. The line scan camera may be configured to capture image data of a sample as a plurality of image stripes via the objective lens. The communication port provides communication over a network. The processor may align the plurality of image stripes into a contiguous image of at least a portion of the sample, and executes a web server that provides an operator interface over the network to one or more remote devices.

Abstract: Systems and methods for capturing a digital image of a slide using an imaging line sensor and a focusing line sensor. In an embodiment, a beam-splitter is optically coupled to an objective lens and configured to receive one or more images of a portion of a sample through the objective lens. The beam-splitter simultaneously provides a first portion of the one or more images to the focusing sensor and a second portion of the one or more images to the imaging sensor. A processor controls the stage and/or objective lens such that each portion of the one or more images is received by the focusing sensor prior to it being received by the imaging sensor. In this manner, a focus of the objective lens can be controlled using data received from the focusing sensor prior to capturing an image of a portion of the sample using the imaging sensor.

Abstract: Systems and methods for capturing image data using a line scan camera. In an embodiment, a line scan camera captures image data of a sample as a plurality of image stripes. A processor may coarsely align two or more of the plurality of image stripes according to a synchronization process while the line scan camera is capturing at least one of the plurality of image stripes. Subsequently, the processor may also finely align the two or more image stripes using pattern matching.

Abstract: A system for collaborative viewing of a digital slide image. In an embodiment, a session is established for viewing a digital slide image by a plurality of client viewers. A leader client viewer and non-leader client viewers are identified for the session. When a command is received from the leader client viewer, the command is sent to each of the non-leader client viewers to synchronize a view of the digital slide image at the non-leader client viewers with the view of the digital slide image at the leader client viewer.

Abstract: An improved diagnostic resolution of digital slide images is obtained by scanning a first digital slide image at diagnostic resolution that is then deconvolved into separate images with one stain per image. The single stain images are then enhanced with image adjustments and/or processed with image analysis algorithms. The resulting single image data sets from the image analysis algorithms can then be stored. Additionally, the resulting enhanced single images can be recombined into a second digital slide image at diagnostic resolution that is also enhanced.

Abstract: Systems, methods, and media for storing a digital image using the Digital Imaging and Communication in Medicine (DICOM) standard. In an embodiment, a digital image at a first resolution is divided into a plurality of regions. Each of the plurality of regions is stored as a separate DICOM image file. In addition, each of the DICOM image files is associated with a DICOM series representing the digital image at the first resolution.

Abstract: Systems, methods, and media for assessing the quality of a microscope slide image. In an embodiment, a plurality of focus point values are acquired for a sample on a microscope slide. Each focus point value comprises x-y coordinates indicating a location on the sample and a z coordinate indicating a focus height for the location on the sample. A best-fit surface is calculated based on the focus point values, and it is determined whether or not outlying focus point values exist based on the best-fit surface and the z coordinate for one or more of the focus point values. A scanned image of the microscope slide may be displayed which comprises, for each outlying focus point value, an overlay that identifies the location on the sample of the outlying focus point value based on the x-y coordinates for the outlying focus point value.

Abstract: A system for creating a contiguous digital image of a fluorescence microscope sample. In an embodiment, the system comprises a both a macro camera and a time delay integration (TDI) line scan camera. The system may also comprise a motorized stage, an illumination module, a light source, an excitation filter, an objective lens, an emission filter, and at least one processor configured to assemble a plurality of digital images of portions of the fluorescence microscope sample, generated by the TDI line scan camera, into a contiguous digital image of at least a portion of the fluorescence microscope sample.

Abstract: Systems and methods for capturing image data using a line scan camera. In an embodiment, a line scan camera captures image data of a sample as a plurality of image stripes. A processor may coarsely align two or more of the plurality of image stripes according to a synchronization process while the line scan camera is capturing at least one of the plurality of image stripes. Subsequently, the processor may also finely align the two or more image stripes using pattern matching.

Abstract: A system for creating a contiguous digital image of a fluorescence microscope sample. In an embodiment, the system comprises a both a macro camera and a time delay integration (TDI) line scan camera. The system may also comprise a motorized stage, an illumination module, a light source, an excitation filter, an objective lens, an emission filter, and at least one processor configured to assemble a plurality of digital images of portions of the fluorescence microscope sample, generated by the TDI line scan camera, into a contiguous digital image of at least a portion of the fluorescence microscope sample.

Abstract: Microscope slide scanner. In an embodiment the microscope slide scanner comprises a single enclosure unit that includes at least one objective lens, at least one line scan camera, at least one communication port, and at least one processor. The line scan camera may be configured to capture image data of a sample as a plurality of image stripes via the objective lens. The communication port provides communication over a network. The processor may align the plurality of image stripes into a contiguous image of at least a portion of the sample, and executes a web server that provides an operator interface over the network to one or more remote devices.

Abstract: Systems and methods for tracking a slide comprising a tissue sample. In an embodiment, data is received from a Laboratory Information System (LIS) barcode associated with a slide and a proprietary barcode generated by a slide staining system, such as a Ventana slide staining system, to track the slide through the staining process. A new label is printed that contains both the LIS barcode and the proprietary barcode, and is attached to the slide. When the slide is subsequently scanned by a slide scanning system, the slide scanning system reads and decodes the LIS barcode to obtain a LIS barcode value. The LIS barcode value may then be used to retrieve information associated with the slide.

Abstract: Systems and methods for standardizing one or more fluorescence scanning instruments to a reference system by separating the effects of drift and normalization. In an embodiment, a drift image comprising an image of a drift reference slide is captured by a system to be standardized. A drift measurement is calculated using the drift image. A first normalization image comprising an image of a normalization slide is also captured by the system to be standardized. A reference normalization image, also comprising an image of the normalization slide, is captured by a reference system. The first normalization image is compared to the reference normalization image to determine a gamma value and offset value for the system to be standardized.

Abstract: Enhancing color(s) in a digital slide image to increase contrast. In an embodiment, a digital slide image of a tissue sample is acquired. The tissue sample is counterstained, such that the digital slide image comprises an image of a first stain and a second stain. The contrast between the first stain and the second stain is increased to enhance the digital slide image.

Abstract: Systems, methods, and media for providing a view of a digital slide image. In an embodiment, a digital slide image file is accessed. The digital slide image file may comprise a plurality of first image planes representing an image of at least a portion of a slide specimen at varying focal depths. Then, a three-dimensional object is constructed from the digital slide image file. The three-dimensional image object is constructed by determining a surface that crosses two or more of the plurality of first image planes, and determining image data that are interior to the determined surface, based on one or more of the plurality of first image planes. A view is generated from the three-dimensional image object.

Abstract: Systems, methods, and media for storing a digital image using the Digital Imaging and Communication in Medicine (DICOM) standard. In an embodiment, a digital image at a first resolution is divided into a plurality of regions. Each of the plurality of regions is stored as a separate DICOM image file. In addition, each of the DICOM image files is associated with a DICOM series representing the digital image at the first resolution.

Abstract: Systems and methods for microscope slide scanning using multiple sensor arrays that receive imagery data from a single optical axis are provided. A single, high quality, easily obtained microscope objective lens is used to project an image onto two or more sensor arrays. The sensor arrays can be linear or two dimensional and imaging takes place along a single optical axis. Simultaneous sensor acquisition and parallel data processing reduce the image acquisition time by a factor of N, where N represents the number of sensors employed.