Yuanning Zheng

... Hi, I noticed that when scanpy reads the spatial information from the "tisslue_position_list.csv" file of the 10X visium data, the (x,y) coordinate for pixels is flipped: positions.columns = [...

ERROR: Unable to fetch palette, reason: 'cell_type_colors'. Using `None`.

2

When using the `sq.pl.centrality_scores(adata, cluster_key="cell_type")` function, I received this error. Has it been seen before? Did I miss something? ...

Sesame Data cache HM450

6

Hi, I am using the SesameData package to retrieve the manifest for the HM450 array as a GRange object ("EH3675"). However, I was not able to cache the file using...

Import external cell segmentation of H&E images to image container

1

Hi, I want to import cell segmentation results generated from an external software to the image container, then using the `sq.im.calculate_image_features` function to assign the centroids of cells to each...

Thanks for creating this awesome package! For generating the spatial interaction scores, why not returning the z scores calculated from the permutation analysis, but the frequencies of cellular interactions? https://github.com/labsyspharm/scimap/blob/7082470dc5233747efb06797721289c813c0c734/scimap/tools/spatial_interaction.py#L206C1-L207C45