st.pl.static.three_d_plot.three_dims_plots.plot_expression_3D ERROR

[wolfQK]

Hi Author, thank you very much for developing the spateo package — it is really a great and useful tool!

I’m currently trying to visualize the spatial expression of certain genes in a point cloud + mesh model.
My goal is to plot cells that express the target gene in blue, and cells without expression in grey.

I noticed that the functionst.pl.static.three_d_plot.three_dims_plots.plot_expression_3D seems to be able to achieve this.
However, when I tried to use it, I encountered the following error: AttributeError: 'function' object has no attribute 'three_dims_plots'

Could you please advise me on the correct way to call plot_expression_3D to achieve my goal?
Or do you have any alternative suggestions for implementing this functionality in spateo?

I would appreciate your guidance and I’m looking forward to your reply.

Thanks again for your excellent work on this package!
@Xiaojieqiu @YifanLu2000

[YifanLu2000]

Hi @wolfQK, for 3D gene-expression visualization, please see this tutorial: https://spateo-release.readthedocs.io/en/latest/tutorials/notebooks/4_tdr/Interpolations.html.

For convenience, here’s a minimal snippet you can run. You can switch the colormap to anything you like (e.g., "viridis", "plasma", etc.). Hope this helps.

exp = adata[pc_index, gene_name].X.flatten()
st.tdr.add_model_labels(model=pc, labels=exp, key_added=gene_name, where="point_data",inplace=True)
st.pl.three_d_plot(
    model=pc,
    key=gene_name,
    colormap="hot_r",
    opacity=0.5,
    model_style="points",
    jupyter="static",
    cpo='iso'
)