Research on deep learning for histology. The full pipeline is used to decompose large tif histology slides into smaller images (tiles) that can be used for training a deep convolutional neural network which are then used to generate heatmaps of pathology hot spots on input images.
Tool that is used for preprocessing ndpi images into tiff images for entire directories and also
generates training tiles from images annotated using QuPath.
See Tiling directory.
Tool that is used to train deep convolutional nerual networks on a tile dataset
generated from the Tiling tool. Trained models are then used as input for
the Evaluation tool. See Training directory.
Tool that tiles a tissue image and uses a pre-trained deep learning
model to classify the tiles as well as show statistics between control and experimental groups. See Evaluation directory.
This work was supported by the John Templeton Foundation grant number 61174.