lungmask

Automated lung segmentation in CT under presence of severe pathologies

This package provides trained U-net models for lung segmentation. For now, four models are available:

• U-net(R231): This model was trained on a large and diverse dataset that covers a wide range of visual variability. The model performs segmentation on individual slices, extracts the right and left lungs separately, and includes air pockets, tumors, and effusions. The trachea will not be included in the lung segmentation. https://doi.org/10.1186/s41747-020-00173-2

• U-net(LTRCLobes): This model was trained on a subset of the LTRC dataset. The model performs segmentation of individual lung-lobes but yields limited performance when dense pathologies are present or when fissures are not visible at every slice.

• U-net(LTRCLobes_R231): This will run the R231 and LTRCLobes models and fuse the results. False negatives from LTRCLobes will be filled by R231 predictions and mapped to a neighboring label. False positives from LTRCLobes will be removed. The fusing process is computationally intensive and can, depending on the data and results, take up to several minutes per volume.

• U-net(R231CovidWeb)

Examples of the two models applied. Left: U-net(R231), will distinguish between left and right lung and include very dense areas such as effusions (third row), tumor or severe fibrosis (fourth row). Right: U-net(LTRCLobes), will distinguish between lung lobes but will not include very dense areas. LTRCLobes_R231 will fuse LTRCLobes and R231 results. R231CovidWeb is trained with additional COVID-19 data.

Semantics of output:
Two label models (Left-Right):
1 = Right lung
2 = Left lung

Five label models (Lung lobes):
1 = Left upper lobe
2 = Left lower lobe
3 = Right upper lobe
4 = Right middle lobe
5 = Right lower lobe

For more exciting research on lung CT data, check out the website of our research group: https://www.cir.meduniwien.ac.at/research/lung/

Referencing and citing

If you use this code or one of the trained models in your work, please refer to:

Hofmanninger, J., Prayer, F., Pan, J. et al. Automatic lung segmentation in routine imaging is primarily a data diversity problem, not a methodology problem. Eur Radiol Exp 4, 50 (2020). https://doi.org/10.1186/s41747-020-00173-2

This paper contains a detailed description of the dataset used, a thorough evaluation of the U-net(R231) model, and a comparison to reference methods.

Installation

pip install lungmask

or

pip install git+https://github.com/JoHof/lungmask

or via conda

conda install conda-forge::lungmask

On Windows, depending on your setup, it may be necessary to install torch beforehand: https://pytorch.org

Runtime and GPU support

Runtime between CPU-only and GPU-supported inference varies greatly. Using the GPU, processing a volume takes only several seconds, while using CPU-only inference takes several minutes. To make use of the GPU, make sure that your torch installation has CUDA support. In case of CUDA out-of-memory errors, reduce the batchsize to 1 with the optional argument --batchsize 1

Usage

As a command line tool:

lungmask INPUT OUTPUT

If INPUT points to a file, the file will be processed. If INPUT points to a directory, the directory will be searched for DICOM series. The largest volume found (in terms of number of voxels) will be used to compute the lungmask. OUTPUT is the output filename. All ITK formats are supported.

Choose a model:

The U-net(R231) will be used as default. However, you can specify an alternative model such as LTRCLobes...

lungmask INPUT OUTPUT --modelname LTRCLobes

For additional options type:

lungmask -h

As a Python module:

from lungmask import LMInferer
import SimpleITK as sitk

inferer = LMInferer()

input_image = sitk.ReadImage(INPUT)
segmentation = inferer.apply(input_image)  # default model is U-net(R231)

input_image has to be a SimpleITK object.

Load an alternative model like so:

inferer = LMInferer(modelname="R231CovidWeb")

To use the model fusing capability (e.g. LTRCLobes_R231), use:

inferer = LMInferer(modelname='LTRCLobes', fillmodel='R231')

Numpy array support

As of version 0.2.9, numpy arrays are supported as input volumes. This mode assumes the input numpy array has the following format for each axis:

• first axis containing slices
• second axis with chest to back
• third axis with right to left

Limitations

The model works on full slices only. The slice to process has to show the full lung and the lung has to be surrounded by tissue in order to get segmented. However, the model is quite stable to cases with a cropped field of view as long as the lung is surrounded by tissue.

COVID-19 Web

lungmask INPUT OUTPUT --modelname R231CovidWeb

The regular U-net(R231) model works very well for COVID-19 CT scans. However, collections of slices and case reports from the web are often cropped, annotated, or encoded in regular image formats so that the original Hounsfield unit (HU) values can only be estimated. The training data of the U-net(R231CovidWeb) model was augmented with COVID-19 slices that were mapped back from regular imaging formats to HU. The data was collected and prepared by MedSeg (http://medicalsegmentation.com/covid19/). While the regular U-net(R231) showed very good results for these images, there may be cases for which this model will yield slightly improved segmentations. Note that you have to map images back to HU when using images from the web. This blog post describes how you can do that. Alternatively, you can set the --noHU tag.

JPG, PNG and non-HU images

This feature is only available in versions between 0.2.5 and 0.2.14 As of version 0.2.5, these images are supported. Use the --noHU tag if you process images that are not encoded in HU. Keep in mind that the models were trained on proper CT scans encoded in HU. The results on cropped, annotated, very high and very low intensity shifted images may not be very reliable. When using the --noHU tag, only single slices can be processed.