Jupyter Notebook

Spatial

Note

Please see:

This page is for now just a stub.

# !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

ln.track("daeFs3PkquDW0000")
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 connected lamindb: testuser1/test-spatial
 created Transform('daeFs3Pk'), started new Run('en31K8KA') at 2024-12-20 15:07:25 UTC
 notebook imports: bionty==0.53.2 lamindb==0.77.3 matplotlib==3.10.0 scanpy==1.10.4

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/718ebfb317faf72d788acfe5ec9ccd494eea8c7118f7cea299e19ca683155b0c.png
adata = ln.core.datasets.anndata_suo22_Visium10X()
# subset to the same image
adata = adata[adata.obs["img_id"] == "F121_LP1_4LIV"].copy()
adata
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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/02575a8849d0b0d751fd18bfe66664132b7bd67a9b6700454e8bd459782a0ad7.png

Validate annotations

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

curate = ln.Curator.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'
curate.validate()
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 saving validated records of 'var_index'
 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', ...
 "var_index" is validated against Gene.ensembl_gene_id
 mapping "sample" on ULabel.name
!   1 term is not validated: 'WSSS_F_IMMsp9838712'
    → fix typos, remove non-existent values, or save terms via .add_new_from("sample")
False
curate.add_new_from("sample")
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 added 1 record with ULabel.name for "sample": 'WSSS_F_IMMsp9838712'
curate.validate()
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 "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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!    26 unique 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', ...
!    did not create Feature records for 26 non-validated names: 'Age_PCW', 'Digestion time', 'EXP_id', 'Fetal_id', 'Organ', 'SN', 'Visium_Area_id', '_indices', '_scvi_batch', '_scvi_labels', 'array_col', 'array_row', 'img_id', 'in_tissue', 'log1p_n_genes_by_counts', 'log1p_total_counts', 'mt_frac', 'n_genes_by_counts', 'paths', 'pct_counts_in_top_100_genes', ...
artifact_ad.describe()
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Artifact .h5ad/AnnData
├── General
│   ├── .uid = 'Xd4tEvEqbi8JqKFA0000'
│   ├── .size = 9743793
│   ├── .hash = '-mhaV6jtrbJtLHCIphbrHg'
│   ├── .n_observations = 3027
│   ├── .path = 
│   │   /home/runner/work/lamin-usecases/lamin-usecases/docs/test-spatial/.lamindb/Xd4tEvEqbi8JqKFA0000.h5ad
│   ├── .created_by = testuser1 (Test User1)
│   ├── .created_at = 2024-12-20 15:07:36
│   └── .transform = 'Spatial'
├── Dataset features/.feature_sets
│   ├── var191                   [bionty.Gene]                                                       
│   │   CD99                        float                                                               
│   │   CD38                        float                                                               
│   │   CDC27                       float                                                               
│   │   CD79B                       float                                                               
│   │   CDKL5                       float                                                               
│   │   CDK11A                      float                                                               
│   │   CD9                         float                                                               
│   │   CD4                         float                                                               
│   │   CD22                        float                                                               
│   │   CD6                         float                                                               
│   │   CD74                        float                                                               
│   │   CD44                        float                                                               
│   │   CDH1                        float                                                               
│   │   CDK17                       float                                                               
│   │   CDH3                        float                                                               
│   │   CDK13                       float                                                               
│   │   CD84                        float                                                               
│   │   CDC42                       float                                                               
│   │   CDH19                       float                                                               
│   │   CD5L                        float                                                               
│   └── obs1                     [Feature]                                                           
sample                      cat[ULabel]                WSSS_F_IMMsp9838712                      
└── Labels
    └── .ulabels                    ULabel                     WSSS_F_IMMsp9838712                      

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/xE3OSN2voDazhOBn0000.tiff')
 storing artifact 'xE3OSN2voDazhOBn0000' at '/home/runner/work/lamin-usecases/lamin-usecases/docs/test-spatial/.lamindb/xE3OSN2voDazhOBn0000.tiff'
Artifact(uid='xE3OSN2voDazhOBn0000', is_latest=True, description='Suo22 image F121_LP1_4LIV', suffix='.tiff', size=119764004, hash='ZAnyai4Ys01P2fLR_aDIvq', _hash_type='sha1-fl', visibility=1, _key_is_virtual=True, storage_id=1, transform_id=1, run_id=1, created_by_id=1, created_at=2024-12-20 15:07:37 UTC)
collection = ln.Collection([artifact_ad, artifact_img], name="Suo22")
collection.save()
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Collection(uid='OFoFJv8sc6UbVXMd0000', is_latest=True, name='Suo22', hash='2cD_KhRukcNMArq-dfyyhg', visibility=1, created_by_id=1, transform_id=1, run_id=1, created_at=2024-12-20 15:07:37 UTC)
# clean up test instance
!lamin delete --force test-spatial
!rm -r test-flow
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Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.11.11/x64/bin/lamin", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/rich_click/rich_command.py", line 367, in __call__
    return super().__call__(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/rich_click/rich_command.py", line 152, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/lamin_cli/__main__.py", line 209, in delete
    return delete(instance, force=force)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/lamindb_setup/_delete.py", line 102, in delete
    n_objects = check_storage_is_empty(
                ^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/lamindb_setup/core/upath.py", line 836, 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 - delete them prior to deleting the instance
rm: cannot remove 'test-flow': No such file or directory