Machine learning

QuPath is open source software for Quantitative Pathology. QuPath has been developed as a research tool at Queen's University Belfast.

This is the "prediction step" of the Pyxit segmentation model builder. It is a learnable segmentation algorithm based on ground-truth images and segmentation mask. It learns a multiple output pixel classification algorithm. It downloads from Cytomine-Core annotation images+alphamasks from project(s), build a segmentation (pixel classifier) model which is saved locally. Typical application: tumor detection in tissues in histology slides. 

This is a learnable segmentation algorithm based on ground-truth images and segmentation mask. It learns a multiple output pixel classification algorithm. It downloads from Cytomine-Core annotation images+alphamasks from project(s), build a segmentation (pixel classifier) model which is saved locally. Typical application: tumor detection in tissues in histology slides. It is based on "Fast Multi-Class Image Annotation with Random Subwindows and Multiple Output Randomized Trees" http://orbi.ulg.ac.be/handle/2268/12205 and was used in "A hybrid human-computer approach for large-scale image-based measurements using web services and machine learning" http://orbi.ulg.ac.be/handle/2268/162084?locale=en

This module is for applying classification models on objects. It downloads from Cytomine-Core annotation images and coordinate of annotated objects from project(s) and build a annotation classification model which is saved locally. It downloads from Cytomine-Core annotations images from an image (e.g. detected by an object finder), apply a classification model (previously saved locally), and uploads to Cytomine-Core annotation terms (in a userjob layer).

This module is for learning classification models from ground-truth data (supervised learning). It downloads from Cytomine-Core annotation images and coordinate of annotated objects from project(s) and build a annotation classification model which is saved locally.  

It is used by Cytomine DataMining applications: classification_validation, classification_model_builder, classification_prediction, segmentation_model_builder and segmentation_prediction. But it can be run without Cytomine on local data (using dir_ls and dir_ts arguments).