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bgilbert / anonymize-slide

Delete the label from a whole-slide image
GNU General Public License v2.0
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Updated legacy code to python 3 #8

Open grenkoca opened 4 years ago

grenkoca commented 4 years ago

I also tested it on some .svs slides

Tomatenbiss commented 4 years ago

@r3m0chop, @jetic83, @grenkoca: I tested this script (just like the script of @markemus and the script of @r3m0chop) with a couple of slides from my institute. I am testing the results with QuPath and 3DHistech Case Viewer where you can access the label images. In case of a successful anonymization the label image cannot be found and the macro image is cropped so the label is not visible anymore (in the original version of the script) or totally removed (in your python3 scripts).

When I use the script on .ndpi files the anonymization works fine.

The script did not work with .mrsx files (old format). An Error is encountered and the slides still contain the label. This is the output (anonymized slide names):

<_io.TextIOWrapper name='<stderr>' mode='w' encoding='utf-8'> ??????.mrxs: 'utf-8' codec can't decode byte 0xff in position 0: invalid start byte

However, in the next days I will have access to .mrxs files in the new format and will report the results.

grenkoca commented 4 years ago

By 'old format' are you referring to 1.9? If so I could try to find and troubleshoot the issue too. I also should have some 2.2 slides available, so I'll give those a shot today and report back the results. Chances are slim, but is there any chance you could post a link to the old .mrsx slide you're using?

Tomatenbiss commented 4 years ago

So far I did not consider the format version numbers. I only differentiated between overlapping tiles (new format) and non-overlapping tiles (old format). How do you access the version number? If it is SLIDE_VERSION in the slidedat.ini then my .mrxs files have version 01.03.

I unfortunately cannot share the slides.

BTW: You might want to check my pull request to @markemus fork of the original script. It also works on python 3 and my changes allow anonymization of my .mrxs files.