Analyze the collection and save a result

import lamindb as ln
import bionty as bt

ln.track("zzJzdgJ763Dy0000")

→ connected lamindb: testuser1/test-facs

→ created Transform('zzJzdgJ763Dy0000', key='facs4.ipynb'), started new Run('VOYAjyWvoRSBPGTP') at 2025-10-30 19:02:36 UTC

→ notebook imports: bionty==1.8.1 lamindb==1.15a1 scanpy==1.11.5

ln.Collection.to_dataframe()

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	uid	key	description	hash	reference	reference_type	version	is_latest	is_locked	created_at	branch_id	space_id	created_by_id	run_id	meta_artifact_id
id
2	xJCs0YYoYshwjGA60001	My versioned cytometry collection	None	eNSQbRNsjg278G1RwXmqCw	None	None	2	True	False	2025-10-30 19:02:28.356000+00:00	1	1	1	2	None
1	xJCs0YYoYshwjGA60000	My versioned cytometry collection	None	jZ8YvUdZGRwPgfoBQbOg_Q	None	None	1	False	False	2025-10-30 19:02:19.064000+00:00	1	1	1	1	None

collection = ln.Collection.get(key="My versioned cytometry collection", version="2")

adata = collection.load(join="inner")

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/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/anndata/_core/anndata.py:1791: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  utils.warn_names_duplicates("obs")

The AnnData has the reference to the individual files in the .obs annotations:

adata.obs.artifact_uid.cat.categories

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Index(['CNYtRlJCCNsU1Ln50000', 'ETOh6WcbRg6ggd8P0000'], dtype='object')

By default, the intersection of features is used:

adata.var.index

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Index(['CD8', 'CD27', 'Ccr7', 'Cd4', 'CD45RA', 'CD3'], dtype='object')

Let us create a plot:

markers = bt.CellMarker.lookup()

import scanpy as sc

sc.pp.pca(adata)
sc.pl.pca(adata, color=markers.cd8.name, save="_cd8")

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WARNING: saving figure to file figures/pca_cd8.pdf

artifact = ln.Artifact("./figures/pca_cd8.pdf", description="My result on CD8").save()
artifact.view_lineage()

Given the image is part of the notebook, there isn’t an actual need to save it and you can also rely on the report that you’ll create when saving the notebook:

ln.finish()

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

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

╭─ Error ──────────────────────────────────────────────────────────────────────╮
│ '/home/runner/work/lamin-usecases/lamin-usecases/docs/test-facs/.lamindb'    │
│ contains 3 objects - delete them prior to deleting the storage location      │
╰──────────────────────────────────────────────────────────────────────────────╯