cell_properties export as NaN
Closed this issue · 1 comments
mezwick commented
Cell properties (area, eccentricity etc) for an ImageSingleCellData()
object display properly in
ImageSingleCellData().regionprops_table
.
However, when exported to_anndata()
, with...
ImageSingleCellData().to_anndata(cell_properties=True, cell_channel_properties=True)
...cell properties are exported as NaN. The cell_channel_properties
to adata.layers
exports work fine.
My current work around is to therefore only export cell_channel_properties
and add cell_properties
into my adata object as new obs
columns individually
ImageSingleCellData().to_anndata(cell_properties=False, cell_channel_properties=True)
for feature in sc_data.regionprops_table.columns:
adata.obs[feature ] = list(sc_data.regionprops_table[feature ])
Though, I suspect there is a neater solution.
jwindhager commented
Uhm, this sounds like a bug. Will fix asap!