MIC-DKFZ
Spacing for TIF files
Hi! I've been having amazing success with your models! However I have bene ignoring the spacing component a bit in the tif images I am using. I would like to compare the performance of my models if I specify the spacing in the .json file. I understand how to generate the spacing .json file per image but wanted to make sure how the spacing is being read. If I have a TIF file with spacing XY=0.102 um and Z= 1um, does the spacing file need to know it is in microns or do I need to convert to some other unit, such a nanometers or meters? Thanks!
Hi just wanted to follow up on this if there is a recommendation on how to specify spacing for tif files? Thanks!
Generally spacings are entered in millimeters, but in principle there is nothin stopping you from choosing a consistent other scale. (But I would not recommend since it is bad practice)
If you'd ignore the recommendations and choose another scale you can run into issues:
Imagine you have your model developed and then apply it to another dataset where the scale is not in um but in mm --> your model will try to resample to the original spacing and this will end up breaking your model (either 1 voxel becomes about 1k repeats and your images will blow up, or your images will shrink to a single point 1000 -> 1).
So the gist is that you need to be consistent. There are no hard constraints but I'd recommend sticking to the mm standard.
