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**Describe the bug**
Hi there, I'm running the public MERFISH tutorial using spatialdata `0.2.2` and spatialdata_plot `0.2.4` (https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks/…
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Hi!
Thanks for the implementation of this awesome alignment algorithm. I was wondering if this tool could deal with the alignment of MERFISH ST data (eg. https://datadryad.org/stash/dataset/doi:10.…
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Hey Quentin,
Thanks for te very nice tolls you developed.
I'm trying t run it on Merscope data using the Snakemake pipeline, using a custom .yaml file based on your baysor_vizgen.yaml one.
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I've tried with a smaller subset of the gitlab_merfish_lung.h5ad file, but it does not help.
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Hi! I've been using the Brain Knowledge Platform to play with the MERFISH whole mouse brain data, and I have a question about the Sample Id annotation when using the Cell Selection tool. When selectin…
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Using [this](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/napari_rois.html#) tutorial for MERFISH data, I found that the output of polygon_query(sdata, my_napari_an…
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Hi, thank you for developing such an interesting tool. As I understood this method is made for Visium-like data where the transcripts measured per spot. But is it possible to use this tool for MERFISH…
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We should make the usage of datasets more heterogenous across the notebooks in the docs.
Practically:
- [ ] select 1, max 3, small datasets (
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Dear developers,
Thanks for developing this great tool. Can I use this tool for processing merfish data and integrate scRNAseq data with merfish?
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I'm working on tutorial notebooks right now and ran into a minor hiccup when running `sq.gr.spatial_neighbors()`. @giovp already ported the function to work with `spatialdata` (thanks!) but the functi…