I used the merfish data and code in the tutorial and reached the step of bt.tl.fe_fazal2019(sdata, batch_size=50000)
The data obtained is as follows:
sdata
SpatialData object
├── Points
│ ├── 'cell_boundaries_raster': DataFrame with shape: (, 151) (2D points)
│ └── 'transcripts': DataFrame with shape: (, 14) (2D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (181, 13) (2D shapes)
│ ├── 'fluxmap1': GeoDataFrame shape: (181, 2) (2D shapes)
│ ├── 'fluxmap2': GeoDataFrame shape: (181, 2) (2D shapes)
│ ├── 'fluxmap3': GeoDataFrame shape: (181, 2) (2D shapes)
│ ├── 'fluxmap4': GeoDataFrame shape: (181, 2) (2D shapes)
│ ├── 'fluxmap5': GeoDataFrame shape: (181, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (146, 5) (2D shapes)
└── Tables
└── 'table': AnnData (181, 135)
with coordinate systems:
▸ 'global', with elements:
cell_boundaries_raster (Points), transcripts (Points), cell_boundaries (Shapes), fluxmap1 (Shapes), fluxmap2 (Shapes), fluxmap3 (Shapes), fluxmap4 (Shapes), fluxmap5 (Shapes), nucleus_boundaries (Shapes)
As the title suggests, I want to add a column to the transcript data I have obtained to determine which subcellular structure this transcript belongs to. Can Bento do this? This has bothered me for a long time.