Shreya Gaddam

Hi @wangjiawen2013 Thank you for using Tangram! You're right about the source of the negative values i.e., lack of raw counts. @Hejin0701 and I reviewed your issue and it is...

hi @jonathanperrie I couldn't reproduce the error. However, I suspect this issue is related to your conda base environment rather than Tangram. Could you let me know the python version...

Hi @daixinap, Thank you for your interest in Tangram! We're glad you like it! You should be able to map snATAC-seq with spatial data as follows: - Compute mapping anndata...

Hi @cynthier, Yes, definitely! You can improve segmentation on H&E images by using different segmentation algorithms. In the tutorial we use 'watershed' algorithm, you can also use [cellpose](https://squidpy.readthedocs.io/en/stable/external_tutorials/tutorial_cellpose_segmentation.html) or [stardist](https://squidpy.readthedocs.io/en/stable/external_tutorials/tutorial_stardist.html)....

Hi @wdg118, thank you for your interest in Tangram! Can you please elaborate on what you mean by `tg.plot_cell_annotation_sc` and `tg.plot_genes_sc` not working? If there's an error, can you provide...

Hi @iS4i4S , thank you for the work-around! Hi @wdg118 , firstly apologies for the delay in my reply. I'm currently working with Tangram version 1.0.3 and scanpy version 1.9.1...

Hi Will! Yes, the functions in the documentation are newer versions(adapted to work with scanpy plotting functions) of the functions i've shared with you(as an alternative) since the functions in...

Sure, let me know. I'm happy to help. I would like to see the error message in that case as well.

Hi @wdg118, - I'm unable to view the attached image with the output from adata_st.uns.get("spatial", {}).keys(). - The error is because you have to specify the names for coordinates of...

@pakiessling Thank for your interest in Tangram! Also, thank you for finding the solution to this issue! I will review and make the change. Best, Shreya