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anonymize-slide's Introduction

anonymize-slide

This is a program to remove the slide label from whole-slide images in the following formats:

  • Aperio SVS
  • Hamamatsu NDPI
  • 3DHISTECH MRXS

Slide files are modified in place, making this program both fast and potentially destructive. Do not run it on your only copy of a slide.

Download

Examples

Delete the label from slide.mrxs:

anonymize-slide.py slide.mrxs

Delete the label from all NDPI files in the current directory:

anonymize-slide.py *.ndpi

Requirements

  • Python 2.6 or 2.7

License

This program is distributed under the GNU General Public License, version 2.

No Warranty

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the license for more details.

anonymize-slide's People

Contributors

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anonymize-slide's Issues

Moving license from GPL-2.0 to Apache 2.0 License

Hi @bgilbert,

We are interested in using your anonymize-slide in one of our projects. However, we have encountered a licensing issue that prevents us from doing so. We would like to inquire whether you have any plans to change the current license (GPL-2.0) or to convert it to the Apache 2.0 License, which would provide us with more flexibility.

Alternatively, would it be possible for you to grant us a waiver to use your anonymize-slide? This would be immensely beneficial to the community, as it would allow us to continue using this project without any legal complications.

Thank you for your consideration.

NDPI WSIs remain identifiable by image metadata

Working with the anonymize-slide.py code, I realized that the unlabelled output WSI still bears the original name/label in the image metadata, and that metadata is visible e.g. in the “Reference” field of the “Image Info” window in NDP.view2. Therefore, even though the tiff label gets removed from the WSI, the slide remains un-anonymized as it is still identifiable by the image metadata. While this may be a more recent issue than the time of the initial release of the code, I was wondering if there could be an straight-forward solution to this issue so the current NDPI slide images can be completely anonymized.

Remove Metadata such as scan date, image ID

Is there a way to delete certain fields in the scans such as comments or scan date or filename? These metainformation can be considered as PHI, or as non-anonymized data.

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