Hello all,
I am trying to investigate heterogeneity of a specific few genes in a specific region of the brain. However, looking at the metadata files, “gene” and “cell_metadata” for the Zeng data, I do not see any categorization for specific regions. Is there another file I must use to connect all of this? Thank you for your time and help!
I want to use the imputed data set as the other does not contain my genes of interest.
Hi @SKadar11
This Jupyter notebook shows how to link the individual cells in the Yao et al. 2023 MERFISH dataset to CCF coordinates and regions (you may want to pay particular attention to this section).
Please let us know if anything is unclear or does not work as expected.
Hi Daniel,
Thank you! That is very helpful. If I want to perform a Moran’s I analysis on my given gene in my given brain region, would I perform this analysis in 3D since we have x, y, and z coordinates with the imputed MERFISH dataset? Thanks!
Hi SKadar11,
I don’t recommend to perform Moran’s I analysis in 3D. The data is not true 3D. We collected a section every 200 microns. I suggest to run this kind of analysis on each section separately.
Best,
Michael
Great, thank you for the help!
If I want to create a UMAP for “C57BL6J-638850-imputed-log2.h5ad”, must I transform the data into another logarithmic form? Are there necessary steps of changing the data prior to plotting. Would this be similar if I just want to make a plot comparing expression of a few genes within a given region? I am very new to computational work and appreciate all of your help. Thank you!