Systems and methods for processing images to determine image-based computational biomarkers from liquid specimens
A method of using machine learning to output task-specific predictions may include receiving a digitized cytology image of a cytology sample and applying a machine learning model to isolate cells of the digitized cytology image. The machine learning model may include identifying a plurality of sub-portions of the digitized cytology image, identifying, for each sub-portion of the plurality of sub-portions, either background or cell, and determining cell sub-images of the digitized cytology image. Each cell sub-image may comprise a cell of the digitized cytology image, based on the identifying either background or cell. The method may further comprise determining a plurality of features based on the cell sub-images, each of the cell sub-images being associated with at least one of the plurality of features, determining an aggregated feature based on the plurality of features, and training a machine learning model to predict a target task based on the aggregated feature.
1. A computer-implemented method for identifying a specimen category, comprising:
receiving one or more digital images of a cytology specimen at a digital storage device;
isolating one or more cell images using the one or more digital images by isolating a set of individual images of cells within the one or more digital images using a segmentation system and/or a detection system;
extracting at least one cell patch from the one or more digital images;
identifying the at least one cell patch as belonging to either cell or background;
extracting one or more cellular features using the cell images; and
determining a specimen category from the one or more cellular features using a trained output aggregation model.
2. The computer-implemented method of claim 1 , further comprising training the trained output aggregation model by:
receiving one or more training digital images of at least one cytology specimen;
receiving at least one training label for the cytology specimen indicating a categorization system and a category of the cytology specimen;
isolating one or more cell images using the one or more training digital images; and
extracting one or more cellular features from the one or more isolated cell images.
3. The computer-implemented method of claim 2 , wherein training the trained output aggregation model includes training the trained output aggregation model to combine the one or more extracted cellular features using the at least one training label.
4. The computer-implemented method of claim 2 , wherein outputting the specimen category includes outputting a visualization and/or a report of the specimen category.
5. The computer-implemented method of claim 1 , further comprising training at least one of the trained output aggregation model or a trained specimen classification model to classify a specimen type for a cytology specimen.
6. The computer-implemented method of claim 5 , further comprising determining a specimen type from the received one or more digital images using the trained output aggregation model or the trained specimen classification model.
7. The computer-implemented method of claim 1 , wherein the set of individual images of cells are isolated within the cell patch.
8. The computer-implemented method of claim 1 , wherein the segmentation system and/or the detection system is a machine learning model.
9. The computer-implemented method of claim 1 , further comprising:
selecting an appropriate categorization system for the one or more cellular features in the cytology specimen.
10. The computer-implemented method of claim 1 , further comprising combining the one or more cellular features in the cytology specimen into an aggregate assessment to represent the digital cytology image as a whole.
11. The computer-implemented method of claim 1 , further comprising:
notifying a user that the specimen category is available; and
providing the user an option to review a visualization and/or a report of the specimen category.
12. The computer-implemented method of claim 1 , further comprising:
outputting the specimen category to a digital storage device and/or display.
13. A system for identifying a specimen category, comprising:
at least one memory storing instructions; and
at least one processor configured to execute the instructions to perform operations comprising:
receiving one or more digital images of a cytology specimen at a digital storage device;
isolating one or more cell images using the one or more digital images by isolating a set of individual images of cells within the one or more digital images using a segmentation system and/or a detection system;
extracting at least one cell patch from the one or more digital images;
identifying the at least one cell patch as belonging to either cell or background;
extracting one or more cellular features using the cell images; and
determining a specimen category from the one or more cellular features using a trained output aggregation model.
14. The system of claim 13 , wherein the operations further comprise training the trained output aggregation model by:
receiving one or more training digital images of at least one cytology specimen;
receiving at least one training label for the cytology specimen indicating a categorization system and a category of the cytology specimen;
isolating one or more cell images using the one or more training digital images; and
extracting one or more cellular features from the one or more isolated cell images.
15. The system of claim 14 , wherein training the trained output aggregation model includes training the trained output aggregation model to combine the one or more extracted cellular features using the at least one training label.
16. The system of claim 13 , wherein:
the set of individual images of cells are isolated within the cell patch.
17. The system of claim 13 , further comprising at least one of a display or a digital storage device, wherein the operations further comprise outputting the specimen category to the at least one of the display or the digital storage device.
18. A non-transitory computer readable medium storing instructions that, when executed by a processor, cause the processor to perform a method for identifying a specimen category, the method comprising:
receiving one or more digital images of a cytology specimen at a digital storage device;
extracting at least one cell patch from the one or more digital images;
identifying the at least one cell patch as belonging to either cell or background;
isolating one or more cell images using the digital images, wherein isolating the one or more cell images comprises isolating a set of individual images of cells within the cell patch using a segmentation system and/or a detection system;
extracting one or more cellular features using the cell images; and
determining a specimen category from the one or more cellular features using a trained output aggregation model.
19. The non-transitory computer readable medium of claim 18 ,
wherein the set of individual images of cells are isolated within the cell patch.