Closed haesleinhuepf closed 1 year ago
Hi Johannes @jo-mueller ,
I'm wondering what's your opinion here. I tried the above implementation in a branch and you can find an example notebook here. Read the last columns of the two tables there carefully. As far as I can see, the proposed code-change will enable us to use the function in more scenarios, because only some values are NaNs and no error happens.
Let me know what you think! Thanks!
Best, Robert
Hi @haesleinhuepf ,
I think that's very reasonable to do. The NaNs are also already accounted for in the cluster plotter so I wouldn't expect them to do much harm. Also, I like using the mesh average size as a way to standardize the measurement!
Thanks for the feedback @jo-mueller !
Also, I like using the mesh average size as a way to standardize the measurement!
Yeah, I also like it. Unfortunately, this doesn't allow inter-sample comparison. I'll open another issue for this.
I'm wondering if the tools would be easier to use if we suppressed this error and replaced it with a warning. This could be done here:
https://github.com/haesleinhuepf/napari-process-points-and-surfaces/blob/a6c9113b4860917cbf6beb2b6c535e9ecced1d25/napari_process_points_and_surfaces/_quantification.py#L247-L254
By writing something like: