Hannover Medical School COVID-19 image repository

[armiro]

They have a dataset of 172 PNG images. Their original images are DCM and of high-quality, which are then converted to Nifti images and downscaled to be hosted in a GitHub repo:
https://github.com/ml-workgroup/covid-19-image-repository

More images will be added to this repo shortly. They will also add CT scans as well.

[armiro]

Images were added but there are some issues & tips here:

• All images are not COVID-19 positive! as they don't have "is_covid" label or something like that, positive images are distinguished by a rule of thumb explained by repo owner here.
• Some images have patient IDs that are misinterpreted by Excel (~5 images because of the exponential sign e).
• Dataset has 172 images with PNG format as of 12/May/2020. Regarding the guideline mentioned in the issue above, 164 images are COVID-19 positive and 8 images are normal CXRs.
• Images are of high quality but darker than the images in our dataset. Hence, brightness adjustment is important as an augmentation function to be applied here.
• According to the issues in the repo, there are some bugs in calculating admission offsets. There may be some changes to the number of current positive CXRs. I've had a look at the positive images and most of them obviously have patchy opacities and consolidation. Normal images are normal.
• Dr. Cohen's dataset has removed some images from Hannover's imported dataset, and I can't find any specific reason for that. This dataset includes all the images in Hannover's so far
• Many images had black regions out of CXR. The majority of the original images were therefore cropped and some of them were straightened.

[armiro]

The issue is reopened for adding images of the next releases. The next set of images including 21 CXRs are added.

Lack of proper disease labelling is worrying me! For instance, CXR with patient_id=d3fb252e and image_id=88859dc1 has an admission offset of 0 with none of the other metrics reported; while it is assumed COVID-19 positive, CXR does not show specific findings related to pneumonia.

Images must come with radiological description to be viable in terms of labelling. This specific image was added with - add the end of the image name. I recheck all images one by one before adding to our dataset to make sure it has signs of pneumonia but I am not an experienced radiologist though!

I have asked the repo maintainer about this problem here

[danshirron]

Is running Hannover_data_loader.py still needed or its images are integrated in current dataset?
If its needed then there are some overwrites of images on existing dataset when running the script. Is that the expected behaviour?

[armiro]

Hey @danshirron

Nope, not needed. The chest_xray_images/covid19 has all the images included. It is also possible to download all the images at once on the FigShare page.

Regarding the Hannover Dataset, I updated the code based on their second version of the dataset. They might have changed some names, but this dataset has all the needed data from their set.