Hassan-gobara / HEMnet

A neural network software for using Molecular labelling to improve pathological annotation of H and E tissues

HEMnet - Haematoxylin & Eosin and Molecular neural network

Description

A deep learning automated cancer diagnosis software using molecular labelling to improve pathological annotation of Haematoxylin and Eosin (H&E) stained tissue.

Installation

1. Docker

   You can download and run the docker image using the following commands:

   docker pull andrewsu1/hemnet    
   docker run -it andrewsu1/hemnet
   

2. Conda

   Install Openslide (this is necessary to open whole slide images) - download it here

   Create a conda environment from the environment.yml file

   conda env create -f environment.yml
   conda activate HEMnet
   

Usage

Slide Preparation

Name slides in the format: slide_id_TP53 for TP53 slides and slide_id_HandE for H&E slides The TP53 and HandE suffix is used by HEMnet to identify the stain used.

1. Generate training and testing datasets

a. Generate train dataset

python HEMnet_train_dataset.py -b /path/to/base/directory -s relative/path/to/slides -o relative/path/to/output/directory -t relative/path/to/template_slide.svs -v

b. Generate test dataset

python HEMnet_test_dataset.py -b /path/to/base/directory -s /relative/path/to/slides -o /relative/path/to/output/directory -t relative/path/to/template_slide -m tile_mag -a align_mag -c cancer_thresh -n non_cancer_thresh

Other parameters:

• -t is the relative path to the template slide from which all other slides will be normalised against. The template slide should be the same for each step.
• -m is the tile magnification. e.g. if the input is 10 then the tiles will be output at 10x
• -a is the align magnification. Paired TP53 and H&E slides will be registered at this magnification. To reduce computation time we recommend this be less than the tile magnification - a five times downscale generally works well.
• -c cancer threshold to apply to the DAB channel. DAB intensities less than this threshold indicate cancer.
• -n non-cancer threshold to apply to the DAB channel. DAB intensities greater than this threshold indicate no cancer.

2. Train and evaluate model

a. Training model

python train.py -b /path/to/base/directory -t relative/path/to/training_tile_directory -l relative/path/to/validation_tile_directory -o /relative/path/to/output/directory -m cnn_base -g num_gpus -e epochs -a batch_size -s -w -f -v

Other parameters:

• -m is CNN base model. eg. resnet50, vgg16, vgg19, inception_v3 and xception.
• -g is number of GPUs for training.
• -e is training epochs. Default is 100 epochs.
• -a is batch size. Default is 32
• -s is option to save the trained model weights.
• -w is option to used transfer learning. Model will used pre-trained weights from ImageNet at the initial stage.
• -f is fine-tuning option. Model will re-train CNN base.

b. Test model prediction

python test.py -b /path/to/base/directory -t relative/path/to/test_tile_directory -o /relative/path/to/output/directory -w model_weights -m cnn_base -g num_gpus -v

Other parameters:

• -w is path to trained model. eg. trained_model.h5.
• -m is CNN base model (same to training step).
• -g is number of GPUs for prediction.

c. Evaluate model performance and visualise model prediction

python visualisation.py -b /path/to/base/directory -t /relative/path/to/training_output_directory -p /relative/path/to/test_output_directory -o /relative/path/to/output/directory -i sample

Other parameters:

• -t is path to training outputs.
• -p is path to test outputs.
• -i is name of Whole Slide Image for visualisation.

3. Apply model to diagnose new images

python HEMnet_inference.py -s '/path/to/new/HE/Slides/' -o '/path/to/output/directory/' -t '/path/to/template/slide/' -nn '/path/to/trained/model/' -v

Predict on TCGA images with our pretrained model for colorectal cancer using google colab

Results

Citing HEMnet

The Team

Please contact Dr Quan Nguyen ([e-mail]), Andrew Su ([e-mail]), and Xiao Tan ([e-mail]) for issues, suggestions, and we are very welcome to collaboration opportunities.