sophieRAIBAUD

show the mean of several genes in spatial scanpy figure

4

... Hello I would like to plot the "log1p_total_counts" of a **visium transcriptomic dataset** (AnnData object with n_obs × n_vars) using sc.pl.spatial **sc.pl.spatial(adatal, img_key="hires", color=["gene1", "gene2", "gene3"]) -**-> gives 3...

MNN correction on spatial datasets

11

## Description ...hello I am struggling with 2 spatial transcriptomics data to compare, but the 2 tissues were spoted perpendicular to each other I dont know how to pivot the...

codex data

2

hello again, do you plan to integrate CODEX data in squidpy package ? Many thanks Sophie ...

interface with NAPARI

4

## Description hello again :) I am trying to add a point layer to napari in interactive mode. I follow these indications to add cells positions that I got with...

remove spots from spatial transcriptomics

11

## Description ... dear all; I have a data coming from an experiment where the tissus seams to have moved and then I got spots with signal where there is...

colormap is not considered using napari squidpy plugin

8

## Description I can not change the color map of the spatial transcriptomic data in Napari ... ## Minimal reproducible example viewer = napari.Viewer() viewer.add_image( img1, colormap='plasma', name="test", metadata={"adata": adata,...