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Support anndata 12 #338

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449beeb
[FIX] make saving of adata.uns more explicit to be compatible with an…
sophiamaedler Nov 8, 2025
bf87181
unpin dependencies
sophiamaedler Nov 8, 2025
fabc6d6
Merge branch 'main' into support_anndata_12
sophiamaedler Jan 4, 2026
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4 changes: 2 additions & 2 deletions requirements/requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@ psutil
numba
h5py
alphabase
anndata<0.12
spatialdata>=0.3.0,<0.6
anndata
spatialdata>=0.3.0
pyarrow<22.0.0
py-lmd>=1.3.1

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24 changes: 13 additions & 11 deletions src/scportrait/pipeline/extraction.py
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Expand Up @@ -740,17 +740,19 @@ def _initialize_empty_anndata(self) -> None:
adata = AnnData(obs=obs, var=vars)

# add additional metadata to `uns`
adata.uns[f"{self.DEFAULT_NAME_SINGLE_CELL_IMAGES}/n_cells"] = self.num_classes
adata.uns[f"{self.DEFAULT_NAME_SINGLE_CELL_IMAGES}/n_channels"] = self.n_masks + self.n_image_channels
adata.uns[f"{self.DEFAULT_NAME_SINGLE_CELL_IMAGES}/n_masks"] = self.n_masks
adata.uns[f"{self.DEFAULT_NAME_SINGLE_CELL_IMAGES}/n_image_channels"] = self.n_image_channels
adata.uns[f"{self.DEFAULT_NAME_SINGLE_CELL_IMAGES}/image_size"] = self.image_size
adata.uns[f"{self.DEFAULT_NAME_SINGLE_CELL_IMAGES}/normalization"] = self.normalization
adata.uns[f"{self.DEFAULT_NAME_SINGLE_CELL_IMAGES}/normalization_range_lower"] = self.normalization_range[0]
adata.uns[f"{self.DEFAULT_NAME_SINGLE_CELL_IMAGES}/normalization_range_upper"] = self.normalization_range[1]
adata.uns[f"{self.DEFAULT_NAME_SINGLE_CELL_IMAGES}/channel_names"] = channels
adata.uns[f"{self.DEFAULT_NAME_SINGLE_CELL_IMAGES}/channel_mapping"] = np.array(channel_mapping, dtype="<U15")
adata.uns[f"{self.DEFAULT_NAME_SINGLE_CELL_IMAGES}/compression"] = self.compression_type
adata.uns[f"{self.DEFAULT_NAME_SINGLE_CELL_IMAGES}"] = {
"n_cells": self.num_classes,
"n_channels": self.n_masks + self.n_image_channels,
"n_masks": self.n_masks,
"n_image_channels": self.n_image_channels,
"image_size": self.image_size,
"normalization": self.normalization,
"normalization_range_lower": self.normalization_range[0],
"normalization_range_upper": self.normalization_range[1],
"channel_names": channels,
"channel_mapping": np.array(channel_mapping, dtype="<U15"),
"compression": self.compression_type,
}

# write to file
adata.write(self.output_path)
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