This is the official Pytorch implementation of "Lung Segmentation from Chest X-rays using Variational Data Imputation", Raghavendra Selvan et al. 2020

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Deep Learning lungVAE
Overview

README

This is the official Pytorch implementation of "Lung Segmentation from Chest X-rays using Variational Data Imputation", Raghavendra Selvan et al. 2020

lotenet

What is this repository for?

  • Predict lung masks from CXRs
  • Model is trained to predict on PA/AP views
  • Train the models described in the paper
  • v1.0

How do I get set up?

  • Basic Pytorch dependency
  • Tested on Pytorch 1.3, Python 3.6
  • Predict using the pretrained model: python predict.py --data DATA_DIR --model saved_models/lungVAE.pt
  • Download preprocessed CXR data from here
  • Train the model from scratch: python train.py --data DATA_DIR

Using preprocessed diffused masks

  • For speed up, the diffused noise masks are precomputed
  • 200 sample masks are provided in this file
  • Check the dataloader to create more or to compute the masks on the fly
  • It is recommended to use precomputed masks

Usage guidelines

  • Kindly cite our publication if you use any part of the code
@misc{raghav2020lungVAE,
 	title={Lung Segmentation from Chest X-rays using Variational Data Imputation},
	author={Raghavendra Selvan and Erik B. Dam and Nicki Skafte Detlefsen and Sofus Rischel and Kaining Sheng and Mads Nielsen and Akshay Pai},
	howpublished={ICML Workshop on The Art of Learning with Missing Values},
	month={July},
 	note={arXiv preprint arXiv:2020.2005.10052},
	year={2020}}

Who do I talk to?

Thanks

  • For the Kaggle data
  • Jaeger S, Karargyris A, Candemir S, Folio L, Siegelman J, Callaghan F, Xue Z, Palaniappan K, Singh RK, Antani S, Thoma G, Wang YX, Lu PX, McDonald CJ. Automatic tuberculosis screening using chest radiographs. IEEE Trans Med Imaging. 2014 Feb;33(2):233-45. doi: 10.1109/TMI.2013.2284099. PMID: 24108713
  • Candemir S, Jaeger S, Palaniappan K, Musco JP, Singh RK, Xue Z, Karargyris A, Antani S, Thoma G, McDonald CJ. Lung segmentation in chest radiographs using anatomical atlases with nonrigid registration. IEEE Trans Med Imaging. 2014 Feb;33(2):577-90. doi: 10.1109/TMI.2013.2290491. PMID: 24239990
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Comments
  • torch load .pt returns tuple and not dict

    torch load .pt returns tuple and not dict

    Hi, using your .pt file I tried to load it torch.load(args.model,map_location=device) which return a tuple of two tensors and not a dict. As a result net.load_state_dict(torch.load(args.model,map_location=device)) returns an error

    'tuple' object has no attribute 'copy'

    I'm using the earliest compatible torch version with Cuda 10.1 which is 1.5 - It's impossible to revert my cuda version. Any idea how I can resolve this issue?

    opened by bartmch 2
  • Run error

    Run error

    "Image = TF.rotate(image,angle)" in "dataset.py" reports an error at runtime "TypeError: function takes exactly 1 argument (3 given)" How to solve it, thank you very much!

    opened by yangbing668 1
  • Error from Cuda To CPU

    Error from Cuda To CPU

    In predict.py Line 155 :

    saveMask(f,mask.squeeze(),h,w,hLoc,wLoc,imH,imW,args.no_post)

    should be changed to :

    saveMask(f,mask.squeeze().cpu(),h,w,hLoc,wLoc,imH,imW,args.no_post)

    as in Line 75 : is using numpy so the image should be in memory.

    img = img.data.numpy()

    This happens when you run the predict with GPU.

    opened by amitbcp 0
Owner
Raghav
Assistant Professor @ Machine Learning Section, Kiehn Lab & Data Science Lab, University of Copenhagen
Raghav
GitHub
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