Jupyter Notebook

Spatial

Note

Please see:

This page is for now just a stub.

Install the lamindb Python package:

pip install 'lamindb[jupyter,bionty]'

!lamin init --storage ./test-spatial --schema bionty
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💡 connected lamindb: testuser1/test-spatial

import lamindb as ln
import bionty as bt
import matplotlib.pyplot as plt
import scanpy as sc
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💡 connected lamindb: testuser1/test-spatial

ln.settings.transform.stem_uid = "daeFs3PkquDW"
ln.settings.transform.version = "draft"
ln.track()

💡 notebook imports: bionty==0.44.3 lamindb==0.74.3 matplotlib==3.9.1 scanpy==1.10.2

💡 saved: Transform(uid='daeFs3PkquDW7a3V', version='draft', name='Spatial', key='spatial', type='notebook', created_by_id=1, updated_at='2024-07-26 12:24:41 UTC')

💡 saved: Run(uid='LqnzxNIthbFLPX0ZFngj', transform_id=1, created_by_id=1)

Run(uid='LqnzxNIthbFLPX0ZFngj', started_at='2024-07-26 12:24:41 UTC', is_consecutive=True, transform_id=1, created_by_id=1)

An example spatial dataset

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

This collection 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.core.datasets.file_tiff_suo22()
img = plt.imread(img_path)
plt.imshow(img)
plt.show()
_images/afcacc77f7c930cfac69bed579cf04a0059063515b42b82f0b72e05af60e9f23.png 
adata = ln.core.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")
_images/14a3e49b409ce99a6ac9d8eb5584908456398e31e20922aa6d32635e4bf1cb47.png

Validate annotations

We’ll register the single-cell data and the image as a Collection.

curate = ln.Curate.from_anndata(adata, var_index=bt.Gene.ensembl_gene_id, categoricals={"sample": ln.ULabel.name}, organism="human")
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✅ added 1 record with Feature.name for columns: 'sample'

❗ 26 non-validated categories are not saved in Feature.name: ['mt_frac', 'Age_PCW', 'pct_counts_in_top_500_genes', 'Visium_Area_id', 'EXP_id', 'pct_counts_in_top_200_genes', 'total_cell_abundance', 'total_counts', 'array_row', 'pct_counts_in_top_50_genes', 'sample_id', '_scvi_batch', 'log1p_n_genes_by_counts', 'pct_counts_in_top_100_genes', 'in_tissue', '_scvi_labels', 'Fetal_id', 'array_col', 'Organ', 'img_id', 'paths', '_indices', 'n_genes_by_counts', 'Digestion time', 'log1p_total_counts', 'SN']!
      → to lookup categories, use lookup().columns
      → to save, run add_new_from_columns

✅ added 191 records from public with Gene.ensembl_gene_id for var_index: 'ENSG00000002586', 'ENSG00000004468', 'ENSG00000004897', 'ENSG00000007312', 'ENSG00000008086', 'ENSG00000008128', 'ENSG00000010278', 'ENSG00000010610', 'ENSG00000012124', 'ENSG00000013725', 'ENSG00000019582', 'ENSG00000026508', 'ENSG00000039068', 'ENSG00000059758', 'ENSG00000062038', 'ENSG00000065883', 'ENSG00000066294', 'ENSG00000070831', 'ENSG00000071991', 'ENSG00000073754', ...

curate.validate()

✅ var_index is validated against Gene.ensembl_gene_id

💡 mapping sample on ULabel.name

❗    1 terms is not validated: 'WSSS_F_IMMsp9838712'
      → save terms via .add_new_from('sample')

False

curate.add_new_from('sample')

✅ added 1 record with ULabel.name for sample: 'WSSS_F_IMMsp9838712'

curate.validate()

✅ var_index is validated against Gene.ensembl_gene_id

✅ sample is validated against ULabel.name

True

Register curated artifact

artifact_ad = curate.save_artifact(description="Suo22 Visium10X image F121_LP1_4LIV")
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💡 path content will be copied to default storage upon `save()` with key `None` ('.lamindb/Dlyqp7W9d21knbIo48WH.h5ad')

✅ storing artifact 'Dlyqp7W9d21knbIo48WH' at '/home/runner/work/lamin-usecases/lamin-usecases/docs/test-spatial/.lamindb/Dlyqp7W9d21knbIo48WH.h5ad'

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

✅    191 terms (100.00%) are validated for ensembl_gene_id

✅    linked: FeatureSet(uid='URaLCCaGRoXhSQS0CVdJ', n=191, dtype='float', registry='bionty.Gene', hash='f29u0HJ47KiqdYQuuhNz', created_by_id=1, run_id=1)

💡 parsing feature names of slot 'obs'

✅    1 term (3.70%) is validated for name

❗    26 terms (96.30%) are not validated for name: in_tissue, array_row, array_col, 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, ...

✅    linked: FeatureSet(uid='zTZOkDE0X0Ns7nTPIkgQ', n=1, registry='Feature', hash='4z67TUJvRux7ef-i5X0U', created_by_id=1, run_id=1)

✅ saved 2 feature sets for slots: 'var','obs'

artifact_ad.describe()

Artifact(uid='Dlyqp7W9d21knbIo48WH', description='Suo22 Visium10X image F121_LP1_4LIV', suffix='.h5ad', type='dataset', accessor='AnnData', size=9743793, hash='MRyvckic_gbrV_hHpHOlAQ', hash_type='md5', n_observations=3027, visibility=1, key_is_virtual=True, updated_at='2024-07-26 12:24:54 UTC')
  Provenance
    .created_by = 'testuser1'
    .storage = '/home/runner/work/lamin-usecases/lamin-usecases/docs/test-spatial'
    .transform = 'Spatial'
    .run = '2024-07-26 12:24:41 UTC'
  Labels
    .ulabels = 'WSSS_F_IMMsp9838712'
  Features
    'sample' = 'WSSS_F_IMMsp9838712'
  Feature sets
    'var' = 'CD99', 'CD38', 'CDC27', 'CD79B', 'CDKL5', 'CDK11A', 'CD9', 'CD4', 'CD22', 'CD6', 'CD74', 'CD44', 'CDH1', 'CDK17', 'CDH3', 'CDK13', 'CD84', 'CDC42', 'CDH19', 'CD5L'
    'obs' = 'sample'

Register a collection

artifact_img = ln.Artifact(img_path, description="Suo22 image F121_LP1_4LIV")
artifact_img.save()
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💡 path content will be copied to default storage upon `save()` with key `None` ('.lamindb/cEyqYhBqL3zgg9NBfSHj.tiff')

✅ storing artifact 'cEyqYhBqL3zgg9NBfSHj' at '/home/runner/work/lamin-usecases/lamin-usecases/docs/test-spatial/.lamindb/cEyqYhBqL3zgg9NBfSHj.tiff'

Artifact(uid='cEyqYhBqL3zgg9NBfSHj', description='Suo22 image F121_LP1_4LIV', suffix='.tiff', type='dataset', size=119764004, hash='ZAnyai4Ys01P2fLR_aDIvq', hash_type='sha1-fl', visibility=1, key_is_virtual=True, created_by_id=1, storage_id=1, transform_id=1, run_id=1, updated_at='2024-07-26 12:24:55 UTC')

collection = ln.Collection([artifact_ad, artifact_img], name="Suo22")
collection.save()

Collection(uid='4RcceQJrbxqnunkrk7mv', name='Suo22', hash='8BBgP1aPBOFv9jCebMhG', visibility=1, created_by_id=1, transform_id=1, run_id=1, updated_at='2024-07-26 12:24:55 UTC')

# clean up test instance
!lamin delete --force test-spatial
!rm -r test-flow
Hide code cell output 
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.10.14/x64/bin/lamin", line 8, in <module>
    sys.exit(main())
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/rich_click/rich_command.py", line 367, in __call__
    return super().__call__(*args, **kwargs)
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/rich_click/rich_command.py", line 152, in main
    rv = self.invoke(ctx)
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/lamin_cli/__main__.py", line 105, in delete
    return delete(instance, force=force)
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/lamindb_setup/_delete.py", line 98, in delete
    n_objects = check_storage_is_empty(
  File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/lamindb_setup/core/upath.py", line 779, in check_storage_is_empty
    raise InstanceNotEmpty(message)
lamindb_setup.core.upath.InstanceNotEmpty: Storage /home/runner/work/lamin-usecases/lamin-usecases/docs/test-spatial/.lamindb contains 2 objects ('_is_initialized' ignored) - delete them prior to deleting the instance
['/home/runner/work/lamin-usecases/lamin-usecases/docs/test-spatial/.lamindb/Dlyqp7W9d21knbIo48WH.h5ad', '/home/runner/work/lamin-usecases/lamin-usecases/docs/test-spatial/.lamindb/_is_initialized', '/home/runner/work/lamin-usecases/lamin-usecases/docs/test-spatial/.lamindb/cEyqYhBqL3zgg9NBfSHj.tiff']

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