Abstract: A slide rack inventory and reinsertion system for use with a digital slide scanning apparatus is provided that determines, prior to scanning of glass slides in a slide rack, a status of each slot in the slide rack as properly occupied, improperly occupied, or empty. The system also determines whether a slide that has been removed from the slide rack for processing has been properly reinserted into the slide rack.

Abstract: Graphical user interface for managing a workflow of a slide scanning system. In an embodiment, the graphical user interface comprises a graphical representation of a carousel used by the scanning system. The graphical representation of the carousel comprises a graphical representation of each of a plurality of rack slots, configured to receive slide racks. The graphical representation of the carousel indicates a position of the carousel, and the graphical representation of each of the plurality of rack slots indicates a status of the represented rack slot and/or a slide rack within the represented rack slot.

Abstract: Real-time autofocus. In an embodiment, a scanning apparatus includes an imaging sensor, a focusing sensor, an objective lens, and processor(s) configured to analyze image data captured by the imaging and focusing sensors, and move the objective lens. Real-time autofocus during scanning of a sample is achieved by determining a true-Z value for the objective lens for a point on a sample and for each of a plurality of regions on the sample. The true-Z values and/or surfaces calculated therefrom are used to determine a predicted-Z value for an unscanned region of the sample. The objective lens is adjusted to the predicted-Z value at the beginning of the unscanned region. After scanning the region, a true-Z value is determined for the region and compared to the predicted-Z value. A rescan of the region is initiated if the comparison exceeds a predetermined threshold.

Abstract: Control processes for a slide-scanning system comprising a carousel with a plurality of rack slots configured to receive slide racks via an exposed portion of the scanning system. In an embodiment, initializing the scanning system comprises automatically homing back-end and front-end components, wherein the front-end components comprise the carousel. An inventory of all slide racks in the carousel is automatically generated. If any slide rack was being processed by any back-end components, the slide rack is automatically unloaded into a corresponding rack slot. In addition, the carousel is automatically positioned to expose a starting subset of the rack slots within the exposed portion. This starting subset may comprise a maximum segment of adjacent empty rack slots.

Abstract: A digital scanning apparatus is provided that includes imaging and focusing sensors and a processor to analyze the image data captured by the imaging and focusing sensors and adjust the focus of the scanning apparatus in real time during a scanning operation. The individual pixels of the imaging sensor are all in the same image plane with respect to the optical path of the digital scanning apparatus. The individual pixels of the focusing sensor are each in a different image plane with respect to the optical path, and one pixel of the focusing sensor is on the same image plane as the image sensor. The processor analyzes image data from the imaging sensor and the focusing sensor and determines a distance and direction to adjust the relative position of an objective lens and a stage of the digital scanning apparatus to achieve optimal focus during the scanning operation.

Abstract: Graphical user interface for managing a workflow of a slide scanning system. In an embodiment, the graphical user interface comprises a graphical representation of a carousel used by the scanning system. The graphical representation of the carousel comprises a graphical representation of each of a plurality of rack slots, configured to receive slide racks. The graphical representation of the carousel indicates a position of the carousel, and the graphical representation of each of the plurality of rack slots indicates a status of the represented rack slot and/or a slide rack within the represented rack slot.

Abstract: A stuck slide determination system is provided that determines if a slide (e.g., glass slide), positioned on a scanning stage at the start of the scanning process, gets stuck and does not move along with the scanning stage after the scanning process commences. In an embodiment, the system includes a sensor having a transmitter and receiver that are relatively positioned to detect the presence of the stage or a slide or the absence of the stage or a slide. When the scanning stage begins to move at the start of the scanning process, a processor monitors a signal from the sensor and determines if the slide is improperly positioned after the scanning process has commenced. If the slide is improperly positioned, the processor stops movement of the scanning stage in order to protect the slide from damage.

Abstract: System for acquiring a digital image of a sample on a microscope slide. In an embodiment, the system comprises a stage configured to support a sample, an objective lens having a single optical axis that is orthogonal to the stage, an imaging sensor, and a focusing sensor. The system further comprises at least one beam splitter optically coupled to the objective lens and configured to receive a field of view corresponding to the optical axis of the objective lens, and simultaneously provide at least a first portion of the field of view to the imaging sensor and at least a second portion of the field of view to the focusing sensor. The focusing sensor may simultaneously acquire image(s) at a plurality of different focal distances and/or simultaneously acquire a pair of mirrored images, each comprising pixels acquired at a plurality of different focal distances.

Abstract: Real-time autofocus. In an embodiment, a scanning apparatus includes an imaging sensor, a focusing sensor, an objective lens, and processor(s) configured to analyze image data captured by the imaging and focusing sensors, and move the objective lens. Real-time autofocus during scanning of a sample is achieved by determining a true-Z value for the objective lens for a point on a sample and for each of a plurality of regions on the sample. The true-Z values and/or surfaces calculated therefrom are used to determine a predicted-Z value for an unscanned region of the sample. The objective lens is adjusted to the predicted-Z value at the beginning of the unscanned region. After scanning the region, a true-Z value is determined for the region and compared to the predicted-Z value. A rescan of the region is initiated if the comparison exceeds a predetermined threshold.

Abstract: A slide rack inventory and reinsertion system for use with a digital slide scanning apparatus is provided that determines, prior to scanning of glass slides in a slide rack, a status of each slot in the slide rack as properly occupied, improperly occupied, or empty. The system also determines whether a slide that has been removed from the slide rack for processing has been properly reinserted into the slide rack.

Abstract: A slide rack inventory and reinsertion system for use with a digital slide scanning apparatus is provided that determines, prior to scanning of glass slides in a slide rack, a status of each slot in the slide rack as properly occupied, improperly occupied, or empty. The system also determines whether a slide that has been removed from the slide rack for processing has been properly reinserted into the slide rack.

Abstract: Real-time autofocus. In an embodiment, a scanning apparatus includes an imaging sensor, a focusing sensor, an objective lens, and processor(s) configured to analyze image data captured by the imaging and focusing sensors, and move the objective lens. Real-time autofocus during scanning of a sample is achieved by determining a true-Z value for the objective lens for a point on a sample and for each of a plurality of regions on the sample. The true-Z values and/or surfaces calculated therefrom are used to determine a predicted-Z value for an unscanned region of the sample. The objective lens is adjusted to the predicted-Z value at the beginning of the unscanned region. After scanning the region, a true-Z value is determined for the region and compared to the predicted-Z value. A rescan of the region is initiated if the comparison exceeds a predetermined threshold.

Abstract: Two-pass capture of a macro image. In an embodiment, a scanning apparatus comprises a stage, a high-resolution camera, and a lens that provides a field of view, substantially equal in width to a slide width, to the high-resolution camera. The apparatus also comprises a first illumination system for transmission-mode illumination, and a second illumination system for reflection-mode illumination. Processor(s) move the stage in a first direction to capture a first macro image of a specimen during a single pass while the field of view is illuminated by the first illumination system, and move the stage in a second direction to capture a second macro image of the specimen during a single pass while the field of view is illuminated by the second illumination system. The processor(s) identify artifacts in the second macro image, and, based on those artifacts, correct the first macro image to generate a modified first macro image.

Abstract: A slide rack inventory and reinsertion system for use with a digital slide scanning apparatus is provided that determines, prior to scanning of glass slides in a slide rack, a status of each slot in the slide rack as properly occupied, improperly occupied, or empty. The system also determines whether a slide that has been removed from the slide rack for processing has been properly reinserted into the slide rack.

Abstract: A digital scanning apparatus is provided that includes imaging and focusing sensors and a processor to analyze the image data captured by the imaging and focusing sensors and adjust the focus of the scanning apparatus in real time during a scanning operation. The individual pixels of the imaging sensor are all in the same image plane with respect to the optical path of the digital scanning apparatus. The individual pixels of the focusing sensor are each in a different image plane with respect to the optical path, and one pixel of the focusing sensor is on the same image plane as the image sensor. The processor analyzes image data from the imaging sensor and the focusing sensor and determines a distance and direction to adjust the relative position of an objective lens and a stage of the digital scanning apparatus to achieve optimal focus during the scanning operation.

Abstract: Apparatus and methods for scanning a 2D or 3D image of a specimen without relative Z-axis motion between the specimen and the objective lens. In an embodiment, the apparatus includes a tilted camera having individual lines of pixels. Each line of pixels can be separately processed and is at a different image plane with respect to the stage. The depth of field of each line of pixels abuts, slightly overlaps, or is slightly spaced apart from the adjacent lines of pixels in the tilted camera. The angle of the tilt determines the relationship (abut, overlapping, or spaced) of the adjacent lines of pixels. The individual image lines produced by each line of pixels can be combined into a 3D volume image of a sample. Also, the highest-contrast line at each X-Y location can be combined into an in-focus 2D image of the sample.

Abstract: A stuck slide determination system is provided that determines if a slide (e.g., glass slide), positioned on a scanning stage at the start of the scanning process, gets stuck and does not move along with the scanning stage after the scanning process commences. In an embodiment, the system includes a sensor having a transmitter and receiver that are relatively positioned to detect the presence of the stage or a slide or the absence of the stage or a slide. When the scanning stage begins to move at the start of the scanning process, a processor monitors a signal from the sensor and determines if the slide is improperly positioned after the scanning process has commenced. If the slide is improperly positioned, the processor stops movement of the scanning stage in order to protect the slide from damage.

Abstract: Real-time autofocus. In an embodiment, a scanning apparatus includes an imaging sensor, a focusing sensor, an objective lens, and processor(s) configured to analyze image data captured by the imaging and focusing sensors, and move the objective lens. Real-time autofocus during scanning of a sample is achieved by determining a true-Z value for the objective lens for a point on a sample and for each of a plurality of regions on the sample. The true-Z values and/or surfaces calculated therefrom are used to determine a predicted-Z value for an unscanned region of the sample. The objective lens is adjusted to the predicted-Z value at the beginning of the unscanned region. After scanning the region, a true-Z value is determined for the region and compared to the predicted-Z value. A rescan of the region is initiated if the comparison exceeds a predetermined threshold.

Abstract: A digital scanning apparatus is provided that includes imaging and focusing sensors and a processor to analyze the image data captured by the imaging and focusing sensors and adjust the focus of the scanning apparatus in real time during a scanning operation. The individual pixels of the imaging sensor are all in the same image plane with respect to the optical path of the digital scanning apparatus. The individual pixels of the focusing sensor are each in a different image plane with respect to the optical path, and one pixel of the focusing sensor is on the same image plane as the image sensor. The processor analyzes image data from the imaging sensor and the focusing sensor and determines a distance and direction to adjust the relative position of an objective lens and a stage of the digital scanning apparatus to achieve optimal focus during the scanning operation.