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 :
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 ?
Someone from forum.image.sc gave me the answer to my issue (1) :
"""
Created on Fri Dec 2 12:28:03 2022
@author: zalavadia.ajay@gmail.com
"""
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