spatialdata-io
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Add reader for Stereo-seq files. TODO: - [x] Read cellbin.gef completely - [x] Fix LabelsModel - [x] Fix ShapesModel - [x] `counts_per_cell` present in .obs? - [x] Update `table.obsm["cellBorder"]` -...
I am working with some data with many `.h5ad` files stored in the same directory. Whenever I create a new `SpatialData` object I specify the path to the correct `AnnData`...
I've been given a new dataset where the positions file is in the V1 location `spatial/tissue_positions_list.csv`, but it has a header. Really annoying I know. This ends up causing an...
Hi, I'm getting this error when trying to import Visium HD data. ` --------------------------------------------------------------------------- ImportError Traceback (most recent call last) Cell In[2], line 3 1 import scanpy as sc 2...
https://github.com/scverse/spatialdata-io/blob/e3c53b5d6789bbaec49181f33dfe368170747ce4/src/spatialdata_io/_constants/_constants.py#L247-L249 from the files on the website it doesn't look like there is such filtered counts https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-of-human-lung-cancer-if https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-of-human-crc https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-of-mouse-intestine https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-of-mouse-brain-he cc @timtreis @Farbodch
Hi, I want to load VisiumHD data in a pipeline without any images, is there a way to accomplish this?
after discussion with @LouisK92 and @timtreis we realized it would be useful for spatialdata to also store the probe set used to target mRNA transcripts. Where should that be stored,...
Adding stitching to the CosMX reader. It's also possible to load one FOV only (if desired), and reading the proteins has also been added. This is still a very early...
## Description Nanostring CosMx datasets have a new file export format through TileDB, https://nanostring.com/wp-content/uploads/2023/01/LiverPublicDataRelease.html They no longer give .csv files for expression matrix and metadata. We are able to generate...
Hola! just updated both `spatialdata` and `spatialdata-io` trying to read a generic xenium dataset with the following line, I get the error bellow: ``` sdata = spatialdata_io.xenium( 'Xenium_V1_FFPE_Human_Breast_IDC', morphology_mip=False, morphology_focus=False,...
