Abstract: The present disclosure is directed to a computer system designed to (i) receive a series of images as input; (ii) compute a number of metrics derived from focus features and color separation features within the images; and (iii) evaluate the metrics to return (a) an identification of the most suitable z-layer in a z-stack, given a series of z-layer images in a z-stack; and/or (b) an identification of those image tiles that are more suitable for cellular based scoring by a medical professional, given a series of image tiles from an area of interest of a whole slide scan.

Abstract: A method and system for measuring the alignment between a substrate and a platform upon which it is disposed by using image processing algorithms are described herein. These algorithms automate the detection of edges of a microscope slide and the platform in a digital image. A reference line pattern in an image of the platform can be used to detect platform edges based on a computed location of the reference line pattern in the image.

Abstract: Systems and methods for automatically excluding artifacts from an analysis of a biological specimen image are disclosed. An exemplary method includes obtaining an immunohistochemistry (IHC) image and a control image, determining whether the control image includes one or more artifacts, upon a determination that the control image includes one or more artifacts, identifying one or more artifact regions within the IHC image by mapping the one or more artifacts from the control image to the IHC image, and performing image analysis of the IHC image where any identified artifact regions are excluded from the image analysis.

Abstract: A digital pathology system and associated method and computer program product provide a quantitative analysis of entire tissue slides as well as intuitive, effective, fast, and precise quantification of biomarker expressions across relevant areas of the entire tissue slides. The digital pathology system enables a novel workflow that allows the user to efficiently outline clinically relevant morphology in its entirety, including solid tumor areas. Quantitative analysis results are then efficiently and intuitively provided to the user for all tissue content (i.e., millions of cells) within seconds. This efficiency is made possible by a pre-computation step that computes and stores image analysis results for later retrieval. Visualizing vast amount of data effectively is another component of the system that provides information and confidence to the user about the biomarker expression levels.

Abstract: The present disclosure describes a method of foreground segmentation and nucleus ranking for scoring dual ISH images. The method has been developed to better identify those nuclei, within a selected field of view, that meet the criteria for dual ISH scoring.

Abstract: The disclosure relates to devices, systems and methods for image registration and annotation. The devices include computer software products for aligning whole slide digital images on a common grid and transferring annotations from one aligned image to another aligned image on the basis of matching tissue structure. The systems include computer-implemented systems such as work stations and networked computers for accomplishing the tissue-structure based image registration and cross-image annotation. The methods include processes for aligning digital images corresponding to adjacent tissue sections on a common grid based on tissue structure, and transferring annotations from one of the adjacent tissue images to another of the adjacent tissue images.

Abstract: The present disclosure is directed to a computer system designed to (i) receive a series of images as input; (ii) compute a number of metrics derived from focus features and color separation features within the images; and (iii) evaluate the metrics to return (a) an identification of the most suitable z-layer in a z-stack, given a series of z-layer images in a z-stack; and/or (b) an identification of those image tiles that are more suitable for cellular based scoring by a medical professional, given a series of image tiles from an area of interest of a whole slide scan.

Abstract: A method and system for measuring the alignment between a substrate and a platform upon which it is disposed by using image processing algorithms are described herein. These algorithms automate the detection of edges of a microscope slide and the platform in a digital image. A reference line pattern in an image of the platform can be used to detect platform edges based on a computed location of the reference line pattern in the image.

Abstract: Systems and methods for automatically excluding artifacts from an analysis of a biological specimen image are disclosed. An exemplary method includes obtaining an immunohistochemistry (IHC) image and a control image, determining whether the control image includes one or more artifacts, upon a determination that the control image includes one or more artifacts, identifying one or more artifact regions within the IHC image by mapping the one or more artifacts from the control image to the IHC image, and performing image analysis of the IHC image where any identified artifact regions are excluded from the image analysis.

Abstract: Methods and systems for generating a heat map that reduces bias in selecting FOVs are disclosed. Some disclosed methods include annotating a primary stained image, registering the annotation to a secondary serial specific stained image, using an image analysis algorithm to compute a scoring criteria specific to the tissue and assay type for tiled regions in the image, using a sliding window in the annotated tumor region to compute values for each pixel in a heat map which correlate to the specific scoring criteria, displaying the heat map at low resolution, ranking and selecting hot spots, selecting FOVs from the hot spot regions which results in displaying the slide-level score for the FOVs. The systems comprise, among other things, software configured to perform the referenced method.

Abstract: A method and associated method and computer program product for acquiring focused images of a specimen on a slide, by determining optimal scanning trajectories. The method includes capturing a relatively low magnification image of the slide to locate the specimen, forming a grid that includes an arrangement of grid points, overlaying at least part of the grid over a field of view that covers at least part of the specimen, capturing a relatively high magnification Z-stack of images of the specimen within the field of view, determining a best focus for each grid point within said at least part of the grid to form a resulting grid of three dimensional points, and based on the resulting grid, determining one or more three dimensional scanning trajectories.

Abstract: The present disclosure describes a method of foreground segmentation and nucleus ranking for scoring dual ISH images. The method has been developed to better identify those nuclei, within a selected field of view, that meet the criteria for dual ISH scoring.

Abstract: A method and associated method and computer program product for acquiring focused images of a specimen on a slide, by determining optimal scanning trajectories. The method includes capturing a relatively low magnification image of the slide to locate the specimen, forming a grid that includes an arrangement of grid points, overlaying at least part of the grid over a field of view that covers at least part of the specimen, capturing a relatively high magnification Z-stack of images of the specimen within the field of view, determining a best focus for each grid point within said at least part of the grid to form a resulting grid of three dimensional points, and based on the resulting grid, determining one or more three dimensional scanning trajectories.

Abstract: Techniques for acquiring focused images of a microscope slide are disclosed. During a calibration phase, a “base” focal plane is determined using non-synthetic and/or synthetic auto-focus techniques. Furthermore, offset planes are determined for color channels (or filter bands) and used to generate an auto-focus model. During subsequent scans, the auto-focus model can be used to quickly estimate the focal plane of interest for each color channel (or filter band) rather than re-employing the non-synthetic and/or synthetic auto-focus techniques.

Abstract: Automated systems and methods for training a multilayer neural network to classify cells and regions from a set of training images are presented. Automated systems and methods for using a trained multilayer neural network to classify cells within an unlabeled image are also presented.

Abstract: The subject disclosure provides systems and methods for determination of Area of Interest (AOI) for different types of input slides. Slide thumbnails may be assigned into one of five different types, and separate algorithms for AOI detection executed depending on the slide type. Slide types include ThinPrep® slides, tissue micro-array (TMA) slides, control HER2 slides with 4 cores, smear slides, and a generic slide. The slide type may be assigned based on a user input. Customized AOI detection operations are provided for each slide type. If the user enters an incorrect slide type, operations include detecting the incorrect input and executing the appropriate method. The result of each AOI detection operations provides as its output a soft-weighted image having zero intensity values at pixels that are detected as not belonging to tissue, and higher intensity values assigned to pixels detected as likely belonging to tissue regions.

Abstract: Automated systems and methods for determining the variability between derived expression scores for a series of biomarkers between different identified cell clusters in a whole slide image are presented. The variability between derived expression scores may be a derived inter-marker heterogeneity metric.

Abstract: The present invention relates to systems and methods for adaptively optimizing broadband reference spectra for a multi-spectral image or adaptively optimizing reference colors for a bright-field image. The methods and systems of the present invention involve optimization techniques that are based on structures detected in an unmixed channel of the image, and involves detecting and segmenting structures from a channel, updating a reference matrix with signals estimated from the structures, subsequently unmixing the image using the updated reference matrix, and iteratively repeating the process until an optimized reference matrix is achieved.

Abstract: Techniques for acquiring focused images of a microscope slide are disclosed. During a calibration phase, a “base” focal plane is determined using non-synthetic and/or synthetic auto-focus techniques. Furthermore, offset planes are determined for color channels (or filter bands) and used to generate an auto-focus model. During subsequent scans, the auto-focus model can be used to quickly estimate the focal plane of interest for each color channel (or filter band) rather than re-employing the non-synthetic and/or synthetic auto-focus techniques.

Abstract: A method and associated method and computer program product for acquiring focused images of a specimen on a slide, by determining optimal scanning trajectories. The method includes capturing a relatively low magnification image of the slide to locate the specimen, forming a grid that includes an arrangement of grid points, overlaying at least part of the grid over a field of view that covers at least part of the specimen, capturing a relatively high magnification Z-stack of images of the specimen within the field of view, determining a best focus for each grid point within said at least part of the grid to form a resulting grid of three dimensional points, and based on the resulting grid, determining one or more three dimensional scanning trajectories.