I'm novice in spatial transcriptomics and I've given an analysis task of merfish ST data, the data consists of different tissue section and I've been asked to focus on certain tissue sections but when I try to do PP and clustering on each tissue separately it gives clusters different than when I try to do PP and clustering on all the tissue sections, so do I have to work on each tissue section separately or work on the entire dataset and then see the observation on each tissue section?
Thanks for your help! I managed to find clusters specific to each section, which align with the literature. Now, I'm stuck because I can't find a Python package that processes and predicts spatial domains in sections. Specifically, I'm looking for a tool that can identify spatial domains in MERFISH data. How are spatial domains typically identified?
Until now, in my lab, this task still heavily requires a pathologist. We also have not been successful in finding assistance from automatic tools.