Abstract: Methods and apparatus are provided for computing focus information during scanning digital microscope slide data with a line scan camera. The systems and methods include a dynamically interleaved procedure that works by moving the specimen relative to the objective lens while the height of the objective lens is adjusted relative to the stage. Imagery data is acquired at a plurality of objective lens heights the image data from the objective lens height having maximum contrast is stored and combined into a composite digital image of at least a portion of the specimen.

Abstract: Systems and methods for managing an image repository for pathology. In an embodiment, a search request is received. One or more digital slide images are identified from an image repository based on the search request. A user is provided access to the identified digital slide images. In addition, each of a plurality of collections of digital slide images are associated with a search rating, and a value for each of the plurality of collections is computed based on the associated search rating and a size of the collection.

Abstract: Systems, methods, and computer-readable media for managing image files over a network. In an embodiment, a notification is received from a remote server. The notification may comprise an identifier of an image file that comprises scanned slide data and is stored at the remote server. In response to the notification, the identifier of the image file may be added in association with an indication that the image file is stored at the remote server to a stored catalog of image files, and a file-transfer operation may be initiated to transfer a copy of the image file from the remote server to a central database. Following completion of the file-transfer operation, the stored catalog may be updated to indicate that the image file is stored in the central database, and a request may be sent to the remote server to delete the image file at the remote server.

Abstract: Systems and methods for analyzing digital slide images. In an embodiment, a digital slide image is acquired from a specimen on a slide. Then, until it is determined that a quality of the digital slide image is sufficient, the quality of the digital slide image is determined and the digital slide image is reacquired. Once it is determined that the quality of the digital slide image is sufficient, the digital slide image and a measure of the quality of the digital slide image is provided to one or more recipients.

Abstract: A portion of imagery data is obtained from a digital slide and a protocol of image analysis/diagnostic tasks is performed on the portion of imagery data by a pathologist or an image analysis module. The result of each task (e.g., success or no success) is recorded and a score is determined for the portion of the imagery data. Multiple portions of imagery data from the digital slide are analyzed and scored and the various scores from the multiple portions of imagery data are calculated to determine an overall score for the digital slide. Regions of the digital slide can be scored separately. Multiple rounds of scoring (by different pathologists and/or different image analysis algorithms) may be employed to increase the accuracy of the score for a digital slide or region thereof.

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 and methods for creating and viewing three dimensional digital slides are provided. One or more microscope slides are positioned in an image acquisition device that scans the specimens on the slides and makes two dimensional images at a medium or high resolution. These two dimensional digital slide images are provided to an image viewing workstation where they are viewed by an operator who pans and zooms the two dimensional image and selects an area of interest for scanning at multiple depth levels (Z-planes). The image acquisition device receives a set of parameters for the multiple depth level scan, including a location and a depth. The image acquisition device then scans the specimen at the location in a series of Z-plane images, where each Z-plane image corresponds to a depth level portion of the specimen within the depth parameter.

Abstract: Methods, media, and systems for assessing the quality of a digital image. In an embodiment, both a micro-analysis and macro-analysis are performed. The micro-analysis comprises dividing the digital image into a plurality of blocks, for two or more of the plurality of blocks, determining a score based on a spatial frequency of the block, and generating a score map for the digital image based on the score for each of the two or more blocks. The macro-analysis comprises detecting artifacts in the digital image, computing a degradation score based on detected artifacts, and computing a whole-slide-quality score based on the score map and the degradation score.

Abstract: Method, systems, and media for processing a digital slide image. In an embodiment, an identification of a macro, representing a plurality of algorithms, and an identification of digital slide image(s) are received over a network. Parameter data is obtained for the identified macro, and the digital slide image(s) are retrieved. The plurality of algorithms represented by the identified macro are executed on the digital slide image(s) according to the parameter data.

Abstract: Systems and methods 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 comprises a plurality of second image planes that are derived from one or more of the first image planes and may comprise at least one image plane that has been interpolated from one or more of the first image planes. In addition, a two-dimensional and/or three-dimensional view of the three-dimensional object may be generated.

Abstract: Systems and methods for creating and viewing three dimensional digital slides are provided. One or more microscope slides are positioned in an image acquisition device that scans the specimens on the slides and makes two dimensional images at a medium or high resolution. These two dimensional digital slide images are provided to an image viewing workstation where they are viewed by an operator who pans and zooms the two dimensional image and selects an area of interest for scanning at multiple depth levels (Z-planes). The image acquisition device receives a set of parameters for the multiple depth level scan, including a location and a depth. The image acquisition device then scans the specimen at the location in a series of Z-plane images, where each Z-plane image corresponds to a depth level portion of the specimen within the depth parameter.

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: Systems and methods for improving quality assurance in pathology using automated quality assessment and digital image enhancements on digital slides prior to analysis by the pathologist are provided. A digital pathology system (slide scanning instrument and software) creates, assesses and improves the quality of a digital slide. The improved digital slide image has a higher image quality that results in increased efficiency and accuracy in the analysis and diagnosis of such digital slides when they are reviewed on a monitor by a pathologist. These improved digital slides yield a more objective diagnosis than reading the corresponding glass slide under a microscope.

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 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: Systems, methods, and computer-readable media for managing image files over a network. In an embodiment, a notification is received from a remote server. The notification may comprise an identifier of an image file that comprises scanned slide data and is stored at the remote server. In response to the notification, the identifier of the image file may be added in association with an indication that the image file is stored at the remote server to a stored catalog of image files, and a file-transfer operation may be initiated to transfer a copy of the image file from the remote server to a central database. Following completion of the file-transfer operation, the stored catalog may be updated to indicate that the image file is stored in the central database, and a request may be sent to the remote server to delete the image file at the remote server.

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: Images created by one or more image acquisition devices are initially stored in remote data bases at one or more remote or satellite locations and copies of the images are subsequently transferred to a central server at a central storage location over a network and stored in a central data base. A common catalog listing local image files stored at the central data base and remote image files stored at one or more remote data bases is stored at the central location and is accessed by users to search for images. User requests for images associated with local image files result in transfer of the requested images by the central server to the user. User requests for images associated with remote image files are relayed by the central server to the associated remote location, and the requested images are then relayed to the user from the remote location via the central server.

Abstract: Systems and methods for assessing and optimizing virtual microscope slide image quality are provided. In order to determine whether any of multiple virtual slide images has an out of focus area and is therefore a candidate for manual inspection or rescanning, various focus points used to scan each virtual slide image are used to calculate a best fit surface for each virtual slide image. The best fit surface is then used to determine whether any of the various focus points are outliers. If it is determined that a virtual slide image is associated with outlying focus points, it is identified as a candidate for manual inspection or rescanning.

Abstract: Systems and methods that acquire digital slides and other large images and store these images into commercially available PACS systems using DICOM-standard messaging are provided. A digital slide or other large two-dimensional image is acquired and each separate resolution level of the digital slide or large image is divided into a series of regions that are each identified as a DICOM image. All of the regions at the same resolution in the digital slide or other large image are collectively identified as a DICOM series. A plurality of DICOM series, representing multiple resolution levels in a digital slide are collectively identified and stored as a DICOM study.