Application on mouse hypothalamic preoptic region MERFISH data

[lvyanzhe]

Dear Professor,

I saw that you mentioned the results on the MERFISH dataset in the supplementary materials. I wonder if you could provide the code applied to the MERFISH dataset? Since I encountered an error while integrating five slices of mouse hypothalamic preoptic region MERFISH data, and I am not sure if it is due to some parameter settings or data preprocessing errors. This error is : ValueError: Found array with 0 sample(s) (shape=(0, 2)) while a minimum of 1 is required by NearestNeighbors.

And it occurred when applying function align_spots, I set the parameters as follows: adata_st_list = STitch3D.utils.align_spots(adata_st_list_raw, data_type="ST",coor_key="loc_use",plot=True,test_all_angles=True)

Thank you so much! Very appreciated!

[JianingYao]

Hi!

Thank you for making this amazing software! I am also wondering where we can find the code for the MERFISH dataset analysis mentioned in the paper and supplementary files. This would be really helpful for adapting to other imaging-based datasets.

Thank you so much, Jianing