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filippocastelli / pyometiff

OME-TIFF IO in python
GNU General Public License v3.0
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Metadata issue when opening in Fiji via drag & drop #16

Open irelamb opened 3 months ago

irelamb commented 3 months ago

Hi Filippo,

I am not sure if you are familiar with ImageJ/Fiji. In case you are, I would share this issue. I have an ome.tif file that was saved via Fiji's Bio-Formats Exporter: when I drag & drop this file in Fiji the metadata are all correct. However, if I drag & drop an ome.tif file saved via your library the metadata are incorrect (I have the impression that Fiji is unable to read the metadata). This issue disappears if instead of drag & drop I import through Bio-Format importer (in that case the metadata are read correctly).

I know it may be something hard to debug, but I was wondering if you had an idea about why it is so.

Thank you and best, Irene

filippocastelli commented 3 months ago

Hey Irene, Usually I test metadata using ImageJ, can you provide me with an image to reproduce the issue?

filippocastelli commented 3 months ago

also, if you encounter metadata issues with a particular file it would be helpful to see if the metadata is correctly encoded using the OME toolkit (https://docs.openmicroscopy.org/ome-model/6.0.1/ome-tiff/tools.html)

tiffcomment path_to_file.ome.tiff | xmlvalid
irelamb commented 3 months ago

Hi Filippo, I shared with you a couple of images on Google drive, I was unable to upload them here. I hope it's ok