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If one subsets an `AnnData` object that has a categorical `obs` column, the new categories of the column will be only the one that appear in the subset column, an not all the original one.
Is this…
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Thank you for resolving the Nextflow script to Bash issue. Resolving this has re-revealed a problem I noticed earlier.
```
[Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing p…
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This issue is to discuss the initial vignettes we want to make in order to demonstrate the utility and usage of SpatialData.
Here are the things I think we want to highlight:
- uniform data API ma…
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I am having trouble following the Merfish tutorial at https://squidpy.readthedocs.io/en/stable/external_tutorials/tutorial_vizgen.html
There, two histograms are ploted to decide on what cells / gen…
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Hi there,
a recent update changed squidpy behavior to no longer put the Merfish "blank_genes" in .var but (I assume) .obsm
Previously I would do something like `sc.pp.calculate_qc_metrics(adata, q…
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Hi dev team.
I tried to select a few visium spots in `adata.obsm['spatial']` and ran into problem that do not understand how coordinates are assigned. I thought that the distance between spots sh…
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## Description
Working on adding a segmentation mask to an ImageContainer with 50+ channels. when using `add_img` an error regarding unable to align different number of channels is thrown back. See…
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Hi,
This is great work! Thanks for your contributions in this field.
I am new to mIF data analysis. I am wondering whether there is an existing standard pipeline for cell type annotation and nei…
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Hi,
I have a question about cell segmentation using Cellpose.
Here's my code stating no GPU while using Cellpose in cell segmentation:
```
def cellpose_he(img, min_size=15, flow_threshold…
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Hi, there.
cell_metadata.csv now has a lot more columns that contain information about protein stainings.
Example columns from my latest measurement:
EntityID,fov,volume,center_x,center_y,…