Ajit Johnson Nirmal
Ajit Johnson Nirmal
hi, @jmuhlich which function were you specifically thinking about? For example, this: https://github.com/labsyspharm/scimap/blob/master/scimap/plotting/_image_viewer.py was implemented with Zaar.
Hi Polo, For most functions in `scimap`, a column named `imageid` is required, which corresponds to a unique identifier for each image. This ensures that during spatial analysis, the XY...
hi @LukasHats I am currently in the middle of working with grant deadlines. I can only investigate this mid October. If you are able to troubleshoot it in the mean...
it is likely due to the computer system that you are using. What are you running it on?
Is this via a HPC? Does it have a GUI component? Could you try Windows or macOS!
Hi, I need to investigate this further, but could you try setting gmm_components=2 and see if that works? That said, the auto-thresholding function is a legacy feature that I’ve been...
Hi @andreevg04, I wouldn't recommend using the auto rescale function in scimap, as it is known to be imperfect, and I've been considering removing it. In our lab, we use...
Interesting. Could it be that the high background levels in CK are contributing to this issue?
hmm can you share your `adata`. If it is large, please subset it to about 10,000 cells.
The measurement is the same as in the X and Y dimensions. If the X and Y dimensions are in pixels (most common form), the measurement indicate distance in pixels....