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Get Started Free →freedomintelligence/bio-spatial-transcriptomics-spatial-multiomics
Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD.
Passed 19 of 22 test cases with the skill, and 14 of 22 without it.
and 6 more in the full report
5 fixed14 passed either way3 still failing0 broke
Tokens, turns and time describe resource use, not a dollar price.
One of 5 test cases the skill fixed. Same model, same prompt, with and without the skill.
How do I plot a spatial scatter plot in Squidpy that uses hexagonal binning shapes with a bin size of 50 colored by cluster?
| Checked | Without skill | With skill |
|---|---|---|
| Calls sq.pl.spatial_scatter with shape='hex'. | Missed | Passed |
| Passes size=50 and color='cluster' to sq.pl.spatial_scatter. | Missed | Passed |
The instructions your model reads when the skill loads.
| Platform | Resolution | Spots/Beads | Coverage |
|---|---|---|---|
| Visium | 55 µm | ~5,000 | Tissue-wide |
| Visium HD | 2 µm | ~11M | Subcellular |
| Slide-seq | 10 µm | ~100,000 | High-density |
| Stereo-seq | 0.5 µm | >200M | Subcellular |
| MERFISH | Single-molecule | N/A | Targeted genes |
import squidpy as sq
import scanpy as sc
# Load spatial data
adata = sc.read_h5ad('spatial_multiomics.h5ad')
# Spatial neighbors (for high-resolution, adjust n_neighs based on density)
sq.gr.spatial_neighbors(adata, coord_type='generic', n_neighs=10, spatial_key='spatial')
# Spatial autocorrelation (Moran's I)
sq.gr.spatial_autocorr(adata, mode='moran', genes=adata.var_names[:100])
test cases passed, vs 14 / 22 without
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