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US 11,908,130 B2Granted
Apparatuses and methods for digital pathology
AssigneeProtein Metrics Inc.
InventorsMichael J. Natan, Marshall Bern, Eric Carlson
Life of this patent
Estimating the term…
Abstract
Digital pathology is a promising alternative to manual slide analysis, but improvements in imaging and analysis methods are needed to provide an analysis data set of images that can easily be handled, stored, and importantly, delivered from one data location to another. Methods and software are described herein to improve image collection and analysis.
Claims19
A method for generating image data for a set of stained slides that comprises a tissue sample, the method comprising:
- selecting a plurality of sub-regions from one of the set of stained slides;
- identifying, for each imaging channel of a first plurality of imaging channels, either a first number of variations of contrast thresholds, a first number of variations of thresholds of marker positivity, or a first number of variations of contrast thresholds and a first number of variations of thresholds of marker positivity, wherein each imaging channel is associated with a corresponding biomarker or plurality of biomarkers;
- generating a plurality of masks for each of the plurality of sub-regions corresponding to each combination of the variations of contrast thresholds and variations of thresholds of marker positivity for each imaging channel of the first plurality of imaging channels, wherein each mask is segmented to identify cells;
- ranking the plurality of masks based on an ability of each of the plurality of masks to accurately identify cells that are positive for the corresponding biomarker or plurality of biomarkers of each imaging channel of the first plurality of imaging channels;
- selecting a set of final mask parameters from the plurality of masks based on the rankings;
- and
- generating a set of slide images for all slides of the set of stained slides using the set of final mask parameters.
4 more elements
A method for generating image data for a set of stained slides that comprises a tissue sample, the method comprising:
- selecting a plurality of sub-regions from one of the set of stained slides, wherein at least one of the sub-regions includes a structure that is substantially free of cells;
- identifying, for each imaging channel of a first plurality of imaging channels:
- a first number of variations of contrast thresholds, a first number of variations of thresholds of marker positivity, or a first number of variations of contrast thresholds and a first number of variations of thresholds of marker positivity, wherein each imaging channel is associated with a corresponding biomarker or plurality of biomarkers;
- generating a plurality of masks comprising a mask for each of the plurality of sub-regions corresponding to each combination of the variations of contrast thresholds and the variations of thresholds of marker positivity for each imaging channel of the first plurality of imaging channels, wherein each mask is segmented to identify cells using the variations of contrast thresholds and the variations of thresholds of marker positivity;
- ranking the plurality of masks based on an ability of each of the plurality of masks to accurately identify cells that are positive for the corresponding biomarker or plurality of biomarkers of each imaging channel of the first plurality of imaging channels;
- selecting a set of final mask parameters from the plurality of masks based on the rankings;
- and
- generating a set of slide images for all slides of the set of stained slides using the set of final mask parameters.
5 more elements
A system for generating image data for a set of stained slides that comprises a tissue sample, the system comprising:
- one or more processors;
- memory coupled to the one or more processors, the memory configured to store computer-program instructions, that, when executed by the one or more processors, perform a computer-implemented method comprising:
- selecting a plurality of sub-regions from one of the set of stained slides;
- identifying, for each imaging channel of a first plurality of imaging channels, either a first number of variations of contrast thresholds, a first number of variations of thresholds of marker positivity, or a first number of variations of contrast thresholds and a first number of variations of thresholds of marker positivity, wherein each imaging channel is associated with a corresponding biomarker or plurality of biomarkers;
- generating a plurality of masks for each of the plurality of sub-regions corresponding to each combination of the variations of contrast thresholds and variations of thresholds of marker positivity for each imaging channel of the first plurality of imaging channels, wherein each mask is segmented to identify cells;
- ranking the plurality of masks based on an ability of each of the plurality of masks to accurately identify cells that are positive for the corresponding biomarker or plurality of biomarkers of each imaging channel of the first plurality of imaging channels;
- selecting a set of final mask parameters from the plurality of masks based on the rankings;
- and
- generating a set of slide images for all slides of the set of stained slides using the set of final mask parameters.
6 more elements
Dependencies are inferred from the claim text.