-
Hi, I am working with the Visium HD colorectal cancer dataset. I have annotated a mask on the microscopic image with qupath and have it as a geoJSON file.
Could I please get instructions/ links to t…
-
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…
-
I've encountered two issues when using the package:
1. Missing Sample Prefix in Output Files:
Our output files do not include a sample prefix, which makes an error when reading the feature_slice.h…
-
### Please describe your wishes and possible alternatives to achieve the desired result.
Hi,
I have a use case in which I am using write_dispatched to perform partial writes of an AnnData object…
-
**User story**
User has transcript coordinates from MERFISH-like experiment that are represented using point elements within a SpatialData object. User wants to visualize these points using Vitessc…
-
Hello!
Would it be possible to any of the following tools:
- Monocle batch correction
- scVI
- CellPhoneDB
- Drug2Cell
- any automated cell annotation tool
(We are keeping a list of request…
-
At some point, the `var_names` and `obs_names` could be something other than strings in Python (See https://github.com/scverse/anndata/issues/777). R data frames can only have characters as rownames, …
-
Because of this line summary stats can be overwritten if two fields use the same name. Summary stats should be a dict with keys being the unique registry keys of the field and values being the summary…
-
Routinely listing improvement we can make to the docs:
- [x] add `rasterize_bins()` example in Visium HD notebook;
- [ ] show how to use `get_element_instances()` in the annotation notebook.
-
Different data:
1. subsets
2. sparse / dense chunks
Also all from disk.