BioImageInformatics / gleason_grade

Code for gleason grading a whole slide in 1 minute or less

Gleason Grade

This project contains the code to train, test, and deploy semantic segmentation models. The training data may be available by request.

If you find this code useful please cite:

bibtex

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Installation

Scripts may be run from the root directory of this project, or from any of the sub-directories. Most of the scripts rely on our tfmodels package for CNN models, or svs_reader package for efficient and extensible reading of SVS format whole slide images.

pip install numpy opencv-contrib-python openslide-python tensorflow-gpu pandas
git clone https://github.com/BioImageInformatics/gleason_grade
cd gleason_grade
git clone https://github.com/BioImageInformatics/svs_reader
git clone https://github.com/BioImageInformatics/tfmodels

Tested on Ubuntu. Python 2.7 and 3.6

Tutorials

1. Creating data from image / mask pairs
2. Training a segmentation network using tfmodels
3. Validating performance on image / mask pairs
4. Applying the model to a whole slide svs image

Directory structure

---

gleason_grade/
|__ data/
    |__ train_jpg (1)
    |__ train_mask (2)
    |__ save_tfrecord.py (3)
    |__ ...misc utility scripts...
|__ densenet/ (4)
    |__ densenet.py (5)
    |__ train.py (6)
    |__ test.py (7)
    |__ experiment_name/ (8)
	|__ logs/ (8a)
	|__ snapshots/ (8b)
	|__ inference/ (8c)
	|__ debug/ (8d)
    ...
|__ densenet_small/
    ...
|__ fcn8s/
...
|__ notebooks/ (9)
|__ tfhub/ (10)
    |__ create_tfhub_training.py (11)
    |__ retrain.py (12)
    |__ deploy_retrained.py (13)
    |__ test_retrained.py (14)
    |__ run_retrain.sh (15)
    |__ run_deploy.sh (16)

1. A directory with source training images
2. A directory with source training masks, name matched to (1)
3. Utility for translating (1) and (2) into tfrecord format for training
4. Model directory. Each model gets its own directory for organizing snapshots and results.
5. The model definition file. This extends one of the base classes in tfmodels
6. Training script. Each model directory has a copy.
7. Testing script. Each model directory has a copy.
8. By default the trained models populate a folder with the structure:
   • a tensorflow logs for visualization via tensorboard
   • b model snapshots for restoring
   • c placeholder for inference outputs generated by this model
   • d placeholder for misc debugging output -- images, masks, etc.
9. A set of jupyter notebooks for running various experiments, and collecting results. Notably, colorize_numpy.ipynb will read the output files in a given directory and produce a color-coded png based on a given color scheme.
10. Tensorflow HUB experiments.
11. Translate images in (1) and (2) into labelled tiles for classifier trainig
12. The retraining script from tensorflow/examples/image_retraining
13. Script to apply retrained Hub modules to SVS files
14. Run a test on retrained Hub classifiers
15. Utility script to hold options for retraining
16. Utility script to hold options for deploy

Notebooks