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Hello,
First, thanks for this great tool!
I am trying to apply it to a somewhat large single cell resolution vizgen dataset of human lung cancer (Vizgen_Human_LungCancer_Patient1) from the MERSC…
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Hi,
I am trying to load the spatial transcriptomics data that are deposited on GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5115019) but as far as I see, the files mapping the barcode…
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Hi team,
Thanks for developing the tool. I think this tool will be super helpful to the community! However, I find that there is no a complete tutorial that can guide me from the raw MERFISH data to …
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Hi,
I specified `segmented_custom` in the following code
```
sq.im.segment(img=img2, layer="image_smooth", channel=None, method=cellpose_he, channel_cellpose=0, flow_threshold=1)
…
WT215 updated
3 months ago
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related to #64 and https://github.com/kevinyamauchi/ome-ngff-tables-prototype , as discussed this morning with @kevinyamauchi this is a description of adata slots and how they are used in https://gith…
giovp updated
2 years ago
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Should we have COMPLEX: in the gene symbol columns as well as the Uniprot columns?
For using squidpy and chinpy, it expects this, so I wrote this code to update the list:
```
intercell_vienna =…
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- [x] Introduction - scope 0.5-1 page
- look into reviews
- broad overview into the field
- mention nature methods "method of the year 2020"
- define axis: targeted/high-resolution vs unbiased…
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## Description
When the `groups`parameter is specified in `sq.pl.spatial_segment` the cells that are plotted are not the cells where `adata.obs[color].isin(groups)`. For example with the `mibitof` …
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There is currently a lack of readily available tools for the presentation of spatial datasets. I would very much like to see a release of this tool that allows you to visualize spatial data either sep…
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## Description
I receive a`TypeError` when proceeding through the Visium florescence tutorial [here](https://squidpy.readthedocs.io/en/stable/notebooks/tutorials/tutorial_visium_fluo.html) when att…