How to edit metadata from .svs Aperio whole slide image?

Question

I have whole slide images, in .svs format, that have be digitized with Leica aperio scan.
Thanks to openslide package (https://openslide.org/), I figured out that those .svs files contain a lot of metadata, especially the ‘Filename’ that can contain patient-related information.
I would like to anonymize completely those metadata, but after several days, I haven’t been able to find a way to do so.

I tried :

svs-deidentifier (https://pearcetm.github.io/svs-deidentifier/)
anonymize-slide (https://github.com/bgilbert/anonymize-slide)
Both of them work very well to remove label and thumbnail from the .svs file, but none of them modify the metadata.

So, I would like to know if it is possible to edit .svs metadata with openslide ? Or any other python package ? Or another third party software (Qupath, imageJ…) ?
Please, could you let me know if you already had this issue ? And if you have any lead in order to adress this question ?

Asked By: chalbiophysics

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Source

Answer 1

Someone from forum.image.sc gave me the answer to my issue (1) :

"""
Created on Fri Dec  2 12:28:03 2022

@author: [email protected]
"""
import tifffile

def replace_filename(svs_path,new_name):
    fp = open(svs_path, 'r+b')
    t = tifffile.TiffFile(fp)
    org_description = t.pages[0].description
    str1 = org_description.split("|Filename = ",1)
    f_name = str1[1].split("|",1)
    print('file name found: ' + f_name[0])
    t.pages[0].tags['ImageDescription'].overwrite(t.pages[0].description.replace(f_name[0],new_name))
    t.pages[1].tags['ImageDescription'].overwrite(t.pages[1].description.replace(f_name[0],new_name))
    fp.close()

replace_filename(‘CMU-1.svs’,’de-identified name’)

Kindly yours

Answered By: chalbiophysics

How to edit metadata from .svs Aperio whole slide image?

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