Questions of the submission template

Questions of the submission template  

  By: eternalaudrey on March 21, 2024, 10:53 p.m.

Hi, I have some questions of the submission template:

  1. In the inference script the tl name is retrieved by using tl = description["OME"]["Image"]["Pixels"]["Channel"]["@Name"]. But seems like this rule is not applicable to all the images. For example, for the image_43_DIC_z5.ome.tiff, the tl name is stored in metadata["OME"]["Image"]["Pixels"]["Channel"]["@Fluor"]. If all the tl names in the testset can be obtained using the same rule?
  2. In terms of the save_image() function, if the provided version is directly applied, there will be an error ValueError: TIFF strings must be 7-bit ASCII. I googled a little bit and found that it can be resolved by replacing description=metadata with description=metadata.encode(). I am not sure if this error is universal?

Thank you!

Re: Questions of the submission template  

  By: danifranco on March 22, 2024, 7:35 a.m.

Hello,

For the 2nd point, I can also confirm that I had the same issue and I solved it as you mentioned with: description=metadata.encode().

Cheers,

 Last edited by: danifranco on March 22, 2024, 8:33 a.m., edited 1 time in total.

Re: Questions of the submission template  

  By: eternalaudrey on March 22, 2024, 10:23 a.m.

thanks for the information :)

Re: Questions of the submission template  

  By: dorian_kauffmann on March 22, 2024, 2:19 p.m.

Hi eternalaudrey,

I checked all Phase 1 input images and the path is well "["OME"]["Image"]["Pixels"]["Channel"]["@Name"]" without exceptions.
Are you sure to have downloaded the last version of the Train Database ? (we provided new links with standardization of all metadata few weeks ago)
I've check image_43_DIC_z5.ome.tiff with ["OME"]["Image"]["Pixels"]["Channel"]["@Name"] and got "DIC".

For the second part I'm agree with @danifranco.