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 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, 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 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: 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, 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: 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: 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: 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 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.

Abstract: Systems and methods for assessing the quality of a digital slide image. In an embodiment, the digital slide image is divided into a plurality of image regions. For each of a subset of the plurality of image regions, a quality of the image region is determined based on a determined spatial frequency of the image region. In addition, a visual depiction of the digital slide image may be generated that, for each of the subset of the plurality of image regions, indicates the determined quality of that image region.

Abstract: Systems and methods for processing, storing, and viewing extremely large imagery data rapidly produced by a linear-array-based microscope slide scanner are provided. The system receives, processes, and stores imagery data produced by the linear scanner as a series of overlapping image stripes and combines the data into a seamless and contiguous baseline image. The baseline image is logically mapped into a plurality of regions that are individually addressed to facilitate viewing and manipulation of the baseline image. The system enables dynamic imagery data compression while scanning and capturing new image stripes that eliminates the overhead associated with storing uncompressed image stripes. The system also creates intermediate level images, thereby organizing the baseline image into a variable level pyramid structure referred to as a virtual slide.

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: A digital slide analysis system comprises an algorithm server that maintains or has access to a plurality of image processing and analysis routines. The algorithm server additionally has access to a plurality of digital slide images. The algorithm server executes a selected routine on an identified digital slide and provides the resulting data. Prior to the application of selected routine, the system employs a digital pre-processing module to create a metadata mask that reduces undesirable image data such that the image data processed by the selected routine has an improved signal to noise ratio. The pre-processing module uses a classifier that may be implemented as a pattern recognition module, for example. Undesirable image data is therefore excluded from the image data that is processed by the digital pathology image processing and analysis routine, which significantly improves the digital pathology image analysis.

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: 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.