Validate & register spatial data

Show code cell content Hide code cell content

!lamin init --storage ./test-spatial --schema bionty

💡 creating schemas: core==0.46.1 bionty==0.30.0 
✅ saved: User(id='DzTjkKse', handle='testuser1', email='testuser1@lamin.ai', name='Test User1', updated_at=2023-08-28 14:46:04)
✅ saved: Storage(id='0xN6cqrl', root='/home/runner/work/lamin-usecases/lamin-usecases/docs/test-spatial', type='local', updated_at=2023-08-28 14:46:05, created_by_id='DzTjkKse')

✅ loaded instance: testuser1/test-spatial
💡 did not register local instance on hub (if you want, call `lamin register`)

import lamindb as ln
import lnschema_bionty as lb
import matplotlib.pyplot as plt
import scanpy as sc

lb.settings.species = "human"
ln.settings.verbosity = 3

Show code cell output Hide code cell output

✅ loaded instance: testuser1/test-spatial (lamindb 0.51.0)

✅ set species: Species(id='uHJU', name='human', taxon_id=9606, scientific_name='homo_sapiens', updated_at=2023-08-28 14:46:08, bionty_source_id='ytbp', created_by_id='DzTjkKse')

ln.track()

💡 notebook imports: lamindb==0.51.0 lnschema_bionty==0.30.0 matplotlib==3.7.2 scanpy==1.9.4

✅ saved: Transform(id='daeFs3PkquDW-R', name='Validate & register spatial data', short_name='spatial', version='draft', type=notebook, updated_at=2023-08-28 14:46:09, created_by_id='DzTjkKse')

✅ saved: Run(id='ilLqGt77bjNoMvhmkMta', run_at=2023-08-28 14:46:09, transform_id='daeFs3PkquDW-R', created_by_id='DzTjkKse')

Here we have a spatial gene expression dataset measured using Visium from Suo22.

This dataset contains two parts:

1. a high-res image of a slice of fetal liver

2. a single cell expression dataset in .h5ad

img_path = ln.dev.datasets.file_tiff_suo22()
img = plt.imread(img_path)
plt.imshow(img)
plt.show()

adata = ln.dev.datasets.anndata_suo22_Visium10X()
# subset to the same image
adata = adata[adata.obs["img_id"] == "F121_LP1_4LIV"].copy()
adata

AnnData object with n_obs × n_vars = 3027 × 191
    obs: 'in_tissue', 'array_row', 'array_col', 'sample', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'pct_counts_in_top_50_genes', 'pct_counts_in_top_100_genes', 'pct_counts_in_top_200_genes', 'pct_counts_in_top_500_genes', 'mt_frac', 'img_id', 'EXP_id', 'Organ', 'Fetal_id', 'SN', 'Visium_Area_id', 'Age_PCW', 'Digestion time', 'paths', 'sample_id', '_scvi_batch', '_scvi_labels', '_indices', 'total_cell_abundance'
    var: 'feature_types', 'genome', 'SYMBOL', 'mt'
    obsm: 'NMF', 'means_cell_abundance_w_sf', 'q05_cell_abundance_w_sf', 'q95_cell_abundance_w_sf', 'spatial', 'stds_cell_abundance_w_sf'

# plot where CD45+ leukocytes are in the slice
sc.pl.scatter(adata, "array_row", "array_col", color="ENSG00000081237")

Register the AnnData and image file as a dataset

file_ad = ln.File.from_anndata(
    adata,
    description="Suo22 Visium10X image F121_LP1_4LIV",
    var_ref=lb.Gene.ensembl_gene_id,
)
file_ad.save()

Show code cell output Hide code cell output

💡 parsing feature names of X stored in slot 'var'

💡    using global setting species = human

❗    191 terms (100.00%) are not validated for ensembl_gene_id: ENSG00000002586, ENSG00000004468, ENSG00000004897, ENSG00000007312, ENSG00000008086, ENSG00000008128, ENSG00000010278, ENSG00000010610, ENSG00000012124, ENSG00000013725, ENSG00000019582, ENSG00000026508, ENSG00000039068, ENSG00000059758, ENSG00000062038, ENSG00000065883, ENSG00000066294, ENSG00000070831, ENSG00000071991, ENSG00000073754, ...

❗    no validated features, skip creating feature set

💡 parsing feature names of slot 'obs'

❗    27 terms (100.00%) are not validated for name: in_tissue, array_row, array_col, sample, n_genes_by_counts, log1p_n_genes_by_counts, total_counts, log1p_total_counts, pct_counts_in_top_50_genes, pct_counts_in_top_100_genes, pct_counts_in_top_200_genes, pct_counts_in_top_500_genes, mt_frac, img_id, EXP_id, Organ, Fetal_id, SN, Visium_Area_id, Age_PCW, ...

❗    no validated features, skip creating feature set

✅ storing file '97woZTq3F1hBTz2BJ91i' at '.lamindb/97woZTq3F1hBTz2BJ91i.h5ad'

file_img = ln.File(img_path, description="Suo22 image F121_LP1_4LIV")
file_img.save()

Show code cell output Hide code cell output

✅ storing file '00KLAop7xZr2ZTJw8eQ3' at '.lamindb/00KLAop7xZr2ZTJw8eQ3.tiff'

dataset = ln.Dataset([file_ad, file_img], name="Suo22")
dataset.save()

Show code cell content Hide code cell content

# clean up test instance
!lamin delete --force test-spatial
!rm -r test-flow

💡 deleting instance testuser1/test-spatial
✅     deleted instance settings file: /home/runner/.lamin/instance--testuser1--test-spatial.env

✅     instance cache deleted
✅     deleted '.lndb' sqlite file
❗     consider manually deleting your stored data: /home/runner/work/lamin-usecases/lamin-usecases/docs/test-spatial

rm: cannot remove 'test-flow': No such file or directory