A U-Net combined with a variational auto-encoder that is able to learn conditional distributions over semantic segmentations.
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Probabilistic U-Net

Re-implementation of the model described in `A Probabilistic U-Net for Segmentation of Ambiguous Images' (arxiv.org/abs/1806.05034).

The architecture of the Probabilistic U-Net is depicted below: subfigure a) shows sampling and b) the training setup:

Below see samples conditioned on held-out validation set images from the (stochastic) CityScapes data set:

Setup package in virtual environment

git clone https://github.com/SimonKohl/probabilistic_unet.git .
cd prob_unet/
virtualenv -p python3 venv
source venv/bin/activate
pip3 install -e .

Install batch-generators for data augmentation

cd ..
git clone https://github.com/MIC-DKFZ/batchgenerators
cd batchgenerators
pip3 install nilearn scikit-image nibabel
pip3 install -e .
cd prob_unet

Download & preprocess the Cityscapes dataset

  1. Create a login account on the Cityscapes website: https://www.cityscapes-dataset.com/
  2. Once you've logged in, download the train, val and test annotations and images:
  3. unzip the data (unzip _trainvaltest.zip) and adjust raw_data_dir (full path to unzipped files) and out_dir (full path to desired output directory) in preprocessing_config.py
  4. bilinearly rescale the data to a resolution of 256 x 512 and save as numpy arrays by running
cd cityscapes
python3 preprocessing.py
cd ..


[skip to evaluation in case you only want to use the pretrained model.]
modify data_dir and exp_dir in scripts/prob_unet_config.py then:

cd training
python3 train_prob_unet.py --config prob_unet_config.py


Load your own trained model or use a pretrained model. A set of pretrained weights can be downloaded from zenodo.org (187MB). After down-loading, unpack the file via tar -xvzf pretrained_weights.tar.gz, e.g. in /model. In either case (using your own or the pretrained model), modify the data_dir and exp_dir in evaluation/cityscapes_eval_config.py to match you paths.

then first write samples (defaults to 16 segmentation samples for each of the 500 validation images):

cd ../evaluation
python3 eval_cityscapes.py --write_samples

followed by their evaluation (which is multi-threaded and thus reasonably fast):

python3 eval_cityscapes.py --eval_samples

The evaluation produces a dictionary holding the results. These can be visualized by launching an ipython notbook:

jupyter notebook evaluation_plots.ipynb

The following results are obtained from the pretrained model using above notebook:


The evaluation metrics are under test-coverage. Run the tests as follows:

cd ../tests/evaluation
python3 -m pytest eval_tests.py

Deviations from original work

The code found in this repository was not used in the original paper and slight modifications apply:

  • training on a single gpu (Titan Xp) instead of distributed training, which is not supported in this implementation
  • average-pooling rather than bilinear interpolation is used for down-sampling operations in the model
  • the number of conv kernels is kept constant after the 3rd scale as opposed to strictly doubling it after each scale (for reduction of memory footprint)
  • HeNormal weight initialization worked better than a orthogonal weight initialization

How to cite this code

Please cite the original publication:

  title={A Probabilistic U-Net for Segmentation of Ambiguous Images},
  author={Kohl, Simon AA and Romera-Paredes, Bernardino and Meyer, Clemens and De Fauw, Jeffrey and Ledsam, Joseph R and Maier-Hein, Klaus H and Eslami, SM and Rezende, Danilo Jimenez and Ronneberger, Olaf},
  journal={arXiv preprint arXiv:1806.05034},


The code is published under the Apache License Version 2.0.