Downstream processing and segmentation visualization

[TatianaSezin]

Hi guys,

just finished generating our first Visium HD data and was very excited to read about ENACT.
I tried to run the output from our HD Visium results in human skin using ENACT. These were the parameters we used:

segmentation: True
bin_to_geodataframes: True
bin_to_cell_assignment: True
cell_type_annotation: True
seg_method: stardist
patch_size: 4000
bin_representation: polygon
bin_to_cell_method: weighted_by_cluster
cell_annotation_method: celltypist
cell_typist_model: Adult_Human_Skin.pkl
use_hvg: True
n_hvg: 1000
n_clusters: 4

We obtained 6 patches. Is there a way to control the number of patches that are generated? Is there a way to visualize the segmentation results? May you please suggest how one should use the ouput from ENACT to continue visualizing the annotated clusters in SquidPy?

Thank you so much in advance for any input and your great support so far!