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You are right, the check on `c_coords` should be one the output data. I merged already because I need to merge #594, which was opened against the current PR. Please can you make a patch for fixing tha…
giovp updated
8 hours ago
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Hi,
Just discovered this really cool package!
I have a question regarding the implementation of Ripleys statistics. What I am interested in is computing e.g. Ripley's K for n subsets of points tha…
giovp updated
2 years ago
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**Question**
Hi
I want to use NCEM for CODEX data , but I could find any tutorial or how to prepare the data for this type of analysis.
Could please direct me if there is any tutorial or n…
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- download a data of choice from 10x genomics with `sc.datasets_visium_sge()` (you can browse them [here](https://support.10xgenomics.com/spatial-gene-expression/datasets))
- run the scanpy tutorial,…
giovp updated
3 years ago
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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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- download a data of choice from 10x genomics with `sc.datasets_visium_sge()` (you can browse them [here](https://support.10xgenomics.com/spatial-gene-expression/datasets))
- run the scanpy tutorial,…
giovp updated
3 years ago
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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
2 months ago
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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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## 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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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