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UniverSeg: Universal Medical Image Segmentation

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Explore UniverSeg in Colab<br>

Official implementation of "UniverSeg: Universal Medical Image Segmentation" accepted at ICCV 2023.

Victor Ion Butoi*, Jose Javier Gonzalez Ortiz*, Tianyu Ma, Mert R. Sabuncu, John Guttag, Adrian V. Dalca,
*denotes equal contribution

network

Given a new segmentation task (e.g. new biomedical domain, new image type, new region of interest, etc), most existing strategies involve training or fine-tuning a segmentation model that takes an image input and outputs the segmentation map.

This process works well in machine-learning labs, but is challenging in many applied settings, such as for scientists or clinical researchers who drive important scientific questions, but often lack the machine-learning expertiese and computational resources necessary.

UniverSeg enables users to tackle a new segmentation task without the need to train or fine-tune a model, removing the requirement for ML experience and computational burden. The key idea is to have a single global model which adapts to a new segmentation task at inference based on an input example set.

Getting Started

The universeg architecture is described in the model.py file. We provide model weights a part of our release.

To instantiate the UniverSeg model (and optionally use provided weights):

from universeg import universeg

model = universeg(pretrained=True)

# To perform a prediction (where B=batch, S=support, H=height, W=width)
prediction = model(
    target_image,        # (B, 1, H, W)
    support_images,      # (B, S, 1, H, W)
    support_labels,      # (B, S, 1, H, W)
) # -> (B, 1, H, W)

For all inputs ensure that pixel values are min-max normalized to the $[0,1]$ range and that the spatial dimensions are $(H, W) = (128, 128)$.

We provide a jupyter notebook with a tutorial and examples of how to do inference using UniverSeg: Google colab | Nbviewer.

Installation

You can install universeg in two ways:

pip install git+https://github.com/JJGO/UniverSeg.git

git clone https://github.com/JJGO/UniverSeg
python -m pip install -r ./UniverSeg/requirements.txt
export PYTHONPATH="$PYTHONPATH:$(realpath ./UniverSeg)"

Citation

If you find our work or any of our materials useful, please cite our paper:

 @article{butoi2023universeg,
  title={UniverSeg: Universal Medical Image Segmentation},
  author={Victor Ion Butoi* and Jose Javier Gonzalez Ortiz* and Tianyu Ma and Mert R. Sabuncu and John Guttag and Adrian V. Dalca},
  journal={International Conference on Computer Vision},
  year={2023}
}

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