sc-imaging

Here, you will learn how to structure, featurize, and make a large imaging collection queryable for large-scale machine learning:

1. Load and annotate a Collection of microscopy images ()

2. Generate single-cell images ()

3. Featurize single-cell images ()

4. Train model to identify autophagy positive cells ()

First, we load and annotate a collection of microscopy images in TIFF format that was previously uploaded.

The images used here were acquired as part of a study on autophagy, a cellular process during which cells recycle their components in autophagosomes. The study tracked genetic determinants of autophagy through fluorescence microscopy of human U2OS cells.

# pip install 'lamindb[jupyter,bionty]'
!lamin init --storage ./test-sc-imaging --modules bionty

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→ initialized lamindb: testuser1/test-sc-imaging

import lamindb as ln
import bionty as bt
from tifffile import imread
import matplotlib.pyplot as plt

ln.track()

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→ connected lamindb: testuser1/test-sc-imaging

→ created Transform('bYTBim7BjUCL0000'), started new Run('4TQVxxtn...') at 2025-06-03 16:30:43 UTC

→ notebook imports: bionty==1.5.0 lamindb==1.6.1 matplotlib==3.10.3 tifffile==2025.6.1

• recommendation: to identify the notebook across renames, pass the uid: ln.track("bYTBim7BjUCL")

All image metadata is stored in an already ingested .csv file on the scportrait/examples instance.

metadata_files = (
    ln.Artifact.using("scportrait/examples")
    .get(key="input_data_imaging_usecase/metadata_files.csv")
    .load()
)

metadata_files.head(2)

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→ transferred records: Artifact(uid='jdjwcUB0w1QAHAYm0000'), Storage(uid='r7YUayXjktSb')

	image_path	genotype	stimulation	cell_line	cell_line_clone	channel	FOV	magnification	microscope	imaged structure	resolution
0	input_data_imaging_usecase/images/Timepoint001...	WT	14h Torin-1	U2OS	U2OS lcklip-mNeon mCherryLC3B clone 1	Alexa488	FOV1	20X	Opera Phenix	LckLip-mNeon	0.597976
1	input_data_imaging_usecase/images/Timepoint001...	WT	14h Torin-1	U2OS	U2OS lcklip-mNeon mCherryLC3B clone 1	Alexa488	FOV2	20X	Opera Phenix	LckLip-mNeon	0.597976

metadata_files.apply(lambda col: col.unique())

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image_path          [input_data_imaging_usecase/images/Timepoint00...
genotype                                                 [WT, EI24KO]
stimulation                                  [14h Torin-1, untreated]
cell_line                                                      [U2OS]
cell_line_clone     [U2OS lcklip-mNeon mCherryLC3B clone 1, U2OS l...
channel                                     [Alexa488, DAPI, mCherry]
FOV                                                      [FOV1, FOV2]
magnification                                                   [20X]
microscope                                             [Opera Phenix]
imaged structure                    [LckLip-mNeon, DNA, mCherry-LC3B]
resolution                                              [0.597976081]
dtype: object

All images are of the same cell line (U2OS), which have been imaged on an Opera Phenix microscope at 20X magnification. To induce autophagy, the cells have either been treated with Torin-1, a small molecule that mimics starvation, for 14 hours, or left untreated as a control.

To visualize the process of autophagosome formation, the U2OS cells have been genetically engineered to express fluorescently tagged proteins. LC3B is a marker of autophagosomes, allowing us to visualize their formation in the mCherry channel. LckLip is a membrane-targeted fluorescent protein, which helps outline the cellular boundaries of individual cells in the Alexa488 channel. Furthermore, the cells’ DNA was stained using Hoechst, which we can visualize in the DAPI channel to identify the nuclei of individual cells.

These three structures are visualized in three separate image channels:

Channel	Imaged Structure
1	DNA
2	Autophagosomes
3	Plasma Membrane

In addition to expressing fluorescently tagged proteins, some of the cells have had the EI24 gene knocked out, leading to two different genotypes: WT (wild-type) cells and EI24KO (knockout) cells. For each genotype, two different clonal cell lines were analyzed, with multiple fields of view (FOVs) captured per condition.

To enable queries on our images, we annotate them with the corresponding metadata.

autophagy_imaging_schema = ln.Schema(
    name="Autophagy imaging schema",
    features=[
        ln.Feature(name="genotype", dtype=ln.ULabel.name).save(),
        ln.Feature(name="stimulation", dtype=ln.ULabel.name).save(),
        ln.Feature(name="cell_line", dtype=bt.CellLine.name).save(),
        ln.Feature(name="cell_line_clone", dtype=ln.ULabel.name).save(),
        ln.Feature(name="channel", dtype=ln.ULabel.name).save(),
        ln.Feature(name="FOV", dtype=ln.ULabel.name).save(),
        ln.Feature(name="magnification", dtype=ln.ULabel.name).save(),
        ln.Feature(name="microscope", dtype=ln.ULabel.name).save(),
        ln.Feature(name="imaged structure", dtype=ln.ULabel.name).save(),
        ln.Feature(
            name="resolution", dtype=float, description="conversion factor for px to µm"
        ).save(),
    ],
    coerce_dtype=True,
).save()

curator = ln.curators.DataFrameCurator(metadata_files, autophagy_imaging_schema)
try:
    curator.validate()
except ln.core.exceptions.ValidationError as e:
    print(e)

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! 2 terms not validated in feature 'genotype': 'WT', 'EI24KO'
    → fix typos, remove non-existent values, or save terms via: curator.cat.add_new_from('genotype')

! 2 terms not validated in feature 'stimulation': '14h Torin-1', 'untreated'
    → fix typos, remove non-existent values, or save terms via: curator.cat.add_new_from('stimulation')

! 1 term not validated in feature 'cell_line': 'U2OS'
    1 synonym found: "U2OS" → "U-2 OS cell"
    → curate synonyms via: .standardize("cell_line")

! 4 terms not validated in feature 'cell_line_clone': 'U2OS lcklip-mNeon mCherryLC3B clone 1', 'U2OS lcklip-mNeon mCherryLC3B clone 2', 'U2OS lcklip-mNeon mCherryLC3B EI24 KO clone 1', 'U2OS lcklip-mNeon mCherryLC3B EI24 KO clone 2'
    → fix typos, remove non-existent values, or save terms via: curator.cat.add_new_from('cell_line_clone')

! 3 terms not validated in feature 'channel': 'Alexa488', 'DAPI', 'mCherry'
    → fix typos, remove non-existent values, or save terms via: curator.cat.add_new_from('channel')

! 2 terms not validated in feature 'FOV': 'FOV1', 'FOV2'
    → fix typos, remove non-existent values, or save terms via: curator.cat.add_new_from('FOV')

! 1 term not validated in feature 'magnification': '20X'
    → fix typos, remove non-existent values, or save terms via: curator.cat.add_new_from('magnification')

! 1 term not validated in feature 'microscope': 'Opera Phenix'
    → fix typos, remove non-existent values, or save terms via: curator.cat.add_new_from('microscope')

! 3 terms not validated in feature 'imaged structure': 'LckLip-mNeon', 'DNA', 'mCherry-LC3B'
    → fix typos, remove non-existent values, or save terms via: curator.cat.add_new_from('imaged structure')

3 terms not validated in feature 'imaged structure': 'LckLip-mNeon', 'DNA', 'mCherry-LC3B'
    → fix typos, remove non-existent values, or save terms via: curator.cat.add_new_from('imaged structure')

Add and standardize missing terms:

curator.cat.standardize("cell_line")
curator.cat.add_new_from("all")
curator.validate()

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! 'all' is deprecated, please pass a single key from `.non_validated.keys()` instead!

! records with similar names exist! did you mean to load one of them?

	uid	name	is_type	description	reference	reference_type	space_id	type_id	run_id	created_at	created_by_id	_aux	branch_id
id
5	9EAQMWeF	U2OS lcklip-mNeon mCherryLC3B clone 1	False	None	None	None	1	None	1	2025-06-03 16:30:51.683000+00:00	1	None	1
6	p1R4W92j	U2OS lcklip-mNeon mCherryLC3B clone 2	False	None	None	None	1	None	1	2025-06-03 16:30:51.683000+00:00	1	None	1
7	ilBy8ry6	U2OS lcklip-mNeon mCherryLC3B EI24 KO clone 1	False	None	None	None	1	None	1	2025-06-03 16:30:51.683000+00:00	1	None	1

! records with similar names exist! did you mean to load one of them?

	uid	name	is_type	description	reference	reference_type	space_id	type_id	run_id	created_at	created_by_id	_aux	branch_id
id
5	9EAQMWeF	U2OS lcklip-mNeon mCherryLC3B clone 1	False	None	None	None	1	None	1	2025-06-03 16:30:51.683000+00:00	1	None	1
6	p1R4W92j	U2OS lcklip-mNeon mCherryLC3B clone 2	False	None	None	None	1	None	1	2025-06-03 16:30:51.683000+00:00	1	None	1
7	ilBy8ry6	U2OS lcklip-mNeon mCherryLC3B EI24 KO clone 1	False	None	None	None	1	None	1	2025-06-03 16:30:51.683000+00:00	1	None	1

Add all images to our lamindb instance to annotate all relevant metadata.

# Create study feature and associated label
ln.Feature(name="study", dtype=ln.ULabel).save()
ln.ULabel(name="autophagy imaging").save()

# loop through all Artifacts and add feature values
artifacts = []
for _, row in metadata_files.iterrows():
    artifact = (
        ln.Artifact.using("scportrait/examples")
        .filter(key__icontains=row["image_path"])
        .one()
    )
    artifact.save()
    artifact.cell_lines.add(bt.CellLine.filter(name=row.cell_line).one())

    artifact.features.add_values(
        {
            "genotype": row.genotype,
            "stimulation": row.stimulation,
            "cell_line_clone": row.cell_line_clone,
            "channel": row.channel,
            "imaged structure": row["imaged structure"],
            "study": "autophagy imaging",
            "FOV": row.FOV,
            "magnification": row.magnification,
            "microscope": row.microscope,
            "resolution": row.resolution,
        }
    )

    artifacts.append(artifact)

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→ transferred records: Artifact(uid='Md4OouMExlWS2YfZ0000'), CellLine(uid='4oLoqaUP'), ULabel(uid='9hHptuyb'), ULabel(uid='A2945i5P'), ULabel(uid='KH1brNUW'), ULabel(uid='XKI9Mx33'), ULabel(uid='CrR7fgIZ'), ULabel(uid='QrU6fxsG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='9hHptuyb'), ULabel(uid='A2945i5P'), ULabel(uid='KH1brNUW'), ULabel(uid='XKI9Mx33'), ULabel(uid='QrU6fxsG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='KKbVRkOjQ1jdA2fx0000'), ULabel(uid='1KPobNqK')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='9hHptuyb'), ULabel(uid='A2945i5P'), ULabel(uid='KH1brNUW'), ULabel(uid='CrR7fgIZ'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='CiQYTBNZrj0CPejK0000'), ULabel(uid='HK8F1lVS'), ULabel(uid='xhpmj7p7')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='HK8F1lVS'), ULabel(uid='9hHptuyb'), ULabel(uid='A2945i5P'), ULabel(uid='KH1brNUW'), ULabel(uid='1KPobNqK'), ULabel(uid='xhpmj7p7'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='W6tzE7JNiM80Ruho0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='9hHptuyb'), ULabel(uid='A2945i5P'), ULabel(uid='KH1brNUW'), ULabel(uid='CrR7fgIZ'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='YGiNq6DPfIEjtt9j0000'), ULabel(uid='AyafKoQw'), ULabel(uid='xHqZKcIG')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='9hHptuyb'), ULabel(uid='A2945i5P'), ULabel(uid='KH1brNUW'), ULabel(uid='AyafKoQw'), ULabel(uid='1KPobNqK'), ULabel(uid='xHqZKcIG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='uuh41FAHEz0ASL2N0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='9hHptuyb'), ULabel(uid='KH1brNUW'), ULabel(uid='XKI9Mx33'), ULabel(uid='CrR7fgIZ'), ULabel(uid='QrU6fxsG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='Gtwi9Pcyx8maQEWB0000'), ULabel(uid='EgihgpJC')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='9hHptuyb'), ULabel(uid='EgihgpJC'), ULabel(uid='KH1brNUW'), ULabel(uid='XKI9Mx33'), ULabel(uid='1KPobNqK'), ULabel(uid='QrU6fxsG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='nSZhAypqiNZ2Ylbe0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='HK8F1lVS'), ULabel(uid='9hHptuyb'), ULabel(uid='EgihgpJC'), ULabel(uid='KH1brNUW'), ULabel(uid='CrR7fgIZ'), ULabel(uid='xhpmj7p7'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='sHHpiiFYWsIXMZNV0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='HK8F1lVS'), ULabel(uid='9hHptuyb'), ULabel(uid='EgihgpJC'), ULabel(uid='KH1brNUW'), ULabel(uid='1KPobNqK'), ULabel(uid='xhpmj7p7'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='jzqxtoduIJ3hCbB40000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='9hHptuyb'), ULabel(uid='EgihgpJC'), ULabel(uid='KH1brNUW'), ULabel(uid='AyafKoQw'), ULabel(uid='CrR7fgIZ'), ULabel(uid='xHqZKcIG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='hNMkrIHce1XrLZHY0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='9hHptuyb'), ULabel(uid='EgihgpJC'), ULabel(uid='KH1brNUW'), ULabel(uid='AyafKoQw'), ULabel(uid='1KPobNqK'), ULabel(uid='xHqZKcIG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='M06liaIzh2OVEuJ40000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='9hHptuyb'), ULabel(uid='A2945i5P'), ULabel(uid='XKI9Mx33'), ULabel(uid='CrR7fgIZ'), ULabel(uid='QrU6fxsG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='yiIMSAddDWgLgki70000'), ULabel(uid='GadMJgvN')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='9hHptuyb'), ULabel(uid='A2945i5P'), ULabel(uid='GadMJgvN'), ULabel(uid='XKI9Mx33'), ULabel(uid='1KPobNqK'), ULabel(uid='QrU6fxsG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='2ie2Kjzn1O7UYhuq0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='HK8F1lVS'), ULabel(uid='9hHptuyb'), ULabel(uid='A2945i5P'), ULabel(uid='GadMJgvN'), ULabel(uid='CrR7fgIZ'), ULabel(uid='xhpmj7p7'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='DEzw4QQAsjVZ010b0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='HK8F1lVS'), ULabel(uid='9hHptuyb'), ULabel(uid='A2945i5P'), ULabel(uid='GadMJgvN'), ULabel(uid='1KPobNqK'), ULabel(uid='xhpmj7p7'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='fOQSb7JCK67aeN6a0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='9hHptuyb'), ULabel(uid='A2945i5P'), ULabel(uid='GadMJgvN'), ULabel(uid='AyafKoQw'), ULabel(uid='CrR7fgIZ'), ULabel(uid='xHqZKcIG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='hbVyCGFARHU91Kax0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='9hHptuyb'), ULabel(uid='A2945i5P'), ULabel(uid='GadMJgvN'), ULabel(uid='AyafKoQw'), ULabel(uid='1KPobNqK'), ULabel(uid='xHqZKcIG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='qHQpdWcFu7FzF6l50000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='9hHptuyb'), ULabel(uid='EgihgpJC'), ULabel(uid='GadMJgvN'), ULabel(uid='XKI9Mx33'), ULabel(uid='CrR7fgIZ'), ULabel(uid='QrU6fxsG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='mXWwV1x42Jz9RoSO0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='9hHptuyb'), ULabel(uid='EgihgpJC'), ULabel(uid='GadMJgvN'), ULabel(uid='XKI9Mx33'), ULabel(uid='1KPobNqK'), ULabel(uid='QrU6fxsG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='Ov8FnKzHMNY0XVJa0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='HK8F1lVS'), ULabel(uid='9hHptuyb'), ULabel(uid='EgihgpJC'), ULabel(uid='GadMJgvN'), ULabel(uid='CrR7fgIZ'), ULabel(uid='xhpmj7p7'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='gj0HHnoVpEqbaUJb0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='HK8F1lVS'), ULabel(uid='9hHptuyb'), ULabel(uid='EgihgpJC'), ULabel(uid='GadMJgvN'), ULabel(uid='1KPobNqK'), ULabel(uid='xhpmj7p7'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='Lwk8shsYe0V5bMgd0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='9hHptuyb'), ULabel(uid='EgihgpJC'), ULabel(uid='GadMJgvN'), ULabel(uid='AyafKoQw'), ULabel(uid='CrR7fgIZ'), ULabel(uid='xHqZKcIG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='1XnEyqVt6UGXCTmV0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='9hHptuyb'), ULabel(uid='EgihgpJC'), ULabel(uid='GadMJgvN'), ULabel(uid='AyafKoQw'), ULabel(uid='1KPobNqK'), ULabel(uid='xHqZKcIG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='YuyVn060M4FxATPz0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='A2945i5P'), ULabel(uid='XKI9Mx33'), ULabel(uid='CrR7fgIZ'), ULabel(uid='QrU6fxsG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='jVytS8AyAHmHkYR30000'), ULabel(uid='Aj8KGwbh'), ULabel(uid='JIbWVXma')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='Aj8KGwbh'), ULabel(uid='A2945i5P'), ULabel(uid='JIbWVXma'), ULabel(uid='XKI9Mx33'), ULabel(uid='1KPobNqK'), ULabel(uid='QrU6fxsG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='vCVbKkzz4CnJPPKF0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='HK8F1lVS'), ULabel(uid='Aj8KGwbh'), ULabel(uid='A2945i5P'), ULabel(uid='JIbWVXma'), ULabel(uid='CrR7fgIZ'), ULabel(uid='xhpmj7p7'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='cw4F6bUB9zuMthCY0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='HK8F1lVS'), ULabel(uid='Aj8KGwbh'), ULabel(uid='A2945i5P'), ULabel(uid='JIbWVXma'), ULabel(uid='1KPobNqK'), ULabel(uid='xhpmj7p7'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='5kMhlcDNek4RMeQF0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='Aj8KGwbh'), ULabel(uid='A2945i5P'), ULabel(uid='JIbWVXma'), ULabel(uid='AyafKoQw'), ULabel(uid='CrR7fgIZ'), ULabel(uid='xHqZKcIG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='7TZGXvbA0JLL68hR0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='Aj8KGwbh'), ULabel(uid='A2945i5P'), ULabel(uid='JIbWVXma'), ULabel(uid='AyafKoQw'), ULabel(uid='1KPobNqK'), ULabel(uid='xHqZKcIG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='9BmbViqMmlVhpfS00000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='Aj8KGwbh'), ULabel(uid='EgihgpJC'), ULabel(uid='JIbWVXma'), ULabel(uid='XKI9Mx33'), ULabel(uid='CrR7fgIZ'), ULabel(uid='QrU6fxsG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='ThuJnRAhqkp54kyU0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='Aj8KGwbh'), ULabel(uid='EgihgpJC'), ULabel(uid='JIbWVXma'), ULabel(uid='XKI9Mx33'), ULabel(uid='1KPobNqK'), ULabel(uid='QrU6fxsG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='h4EKWveW36LIzXez0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='HK8F1lVS'), ULabel(uid='Aj8KGwbh'), ULabel(uid='EgihgpJC'), ULabel(uid='JIbWVXma'), ULabel(uid='CrR7fgIZ'), ULabel(uid='xhpmj7p7'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='PquYNyshQTDd24Vw0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='HK8F1lVS'), ULabel(uid='Aj8KGwbh'), ULabel(uid='EgihgpJC'), ULabel(uid='JIbWVXma'), ULabel(uid='1KPobNqK'), ULabel(uid='xhpmj7p7'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='fdem35nw5ztUnEIM0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='Aj8KGwbh'), ULabel(uid='EgihgpJC'), ULabel(uid='JIbWVXma'), ULabel(uid='AyafKoQw'), ULabel(uid='CrR7fgIZ'), ULabel(uid='xHqZKcIG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='8SFUmW0RhBNySxBO0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='Aj8KGwbh'), ULabel(uid='EgihgpJC'), ULabel(uid='JIbWVXma'), ULabel(uid='AyafKoQw'), ULabel(uid='1KPobNqK'), ULabel(uid='xHqZKcIG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='VkmKLUCaMsYFCuGE0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='Aj8KGwbh'), ULabel(uid='A2945i5P'), ULabel(uid='XKI9Mx33'), ULabel(uid='CrR7fgIZ'), ULabel(uid='QrU6fxsG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='OS0wBE7bviIlW7qj0000'), ULabel(uid='joRCMMWX')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='Aj8KGwbh'), ULabel(uid='A2945i5P'), ULabel(uid='joRCMMWX'), ULabel(uid='XKI9Mx33'), ULabel(uid='1KPobNqK'), ULabel(uid='QrU6fxsG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='9ZVngbl0JUS0XdZ70000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='HK8F1lVS'), ULabel(uid='Aj8KGwbh'), ULabel(uid='A2945i5P'), ULabel(uid='joRCMMWX'), ULabel(uid='CrR7fgIZ'), ULabel(uid='xhpmj7p7'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='ixOpuSTsyrPXdYuA0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='HK8F1lVS'), ULabel(uid='Aj8KGwbh'), ULabel(uid='A2945i5P'), ULabel(uid='joRCMMWX'), ULabel(uid='1KPobNqK'), ULabel(uid='xhpmj7p7'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='IzP3IAwIhmM7OORD0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='Aj8KGwbh'), ULabel(uid='A2945i5P'), ULabel(uid='joRCMMWX'), ULabel(uid='AyafKoQw'), ULabel(uid='CrR7fgIZ'), ULabel(uid='xHqZKcIG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='6uMjKAk1aYlAV7Cf0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='Aj8KGwbh'), ULabel(uid='A2945i5P'), ULabel(uid='joRCMMWX'), ULabel(uid='AyafKoQw'), ULabel(uid='1KPobNqK'), ULabel(uid='xHqZKcIG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='RRVS8qVx3VSw02Xu0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='Aj8KGwbh'), ULabel(uid='EgihgpJC'), ULabel(uid='joRCMMWX'), ULabel(uid='XKI9Mx33'), ULabel(uid='CrR7fgIZ'), ULabel(uid='QrU6fxsG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='QDPX1ljp0eCMz80o0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='Aj8KGwbh'), ULabel(uid='EgihgpJC'), ULabel(uid='joRCMMWX'), ULabel(uid='XKI9Mx33'), ULabel(uid='1KPobNqK'), ULabel(uid='QrU6fxsG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='Oww4y0yYuR8pxV9q0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='HK8F1lVS'), ULabel(uid='Aj8KGwbh'), ULabel(uid='EgihgpJC'), ULabel(uid='joRCMMWX'), ULabel(uid='CrR7fgIZ'), ULabel(uid='xhpmj7p7'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='Cvamog4G3a2XYGM80000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='HK8F1lVS'), ULabel(uid='Aj8KGwbh'), ULabel(uid='EgihgpJC'), ULabel(uid='joRCMMWX'), ULabel(uid='1KPobNqK'), ULabel(uid='xhpmj7p7'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='AhBvnNKg5yJcG6LU0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='Aj8KGwbh'), ULabel(uid='EgihgpJC'), ULabel(uid='joRCMMWX'), ULabel(uid='AyafKoQw'), ULabel(uid='CrR7fgIZ'), ULabel(uid='xHqZKcIG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='6uUjyphUD4D1Hixc0000')

→ mapped records: CellLine(uid='4oLoqaUP'), ULabel(uid='Aj8KGwbh'), ULabel(uid='EgihgpJC'), ULabel(uid='joRCMMWX'), ULabel(uid='AyafKoQw'), ULabel(uid='1KPobNqK'), ULabel(uid='xHqZKcIG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ transferred records: Artifact(uid='AVRTVX9gEu4LrTAP0000')

artifacts[0].describe()

Artifact .tif
├── General
│   ├── .uid = 'Md4OouMExlWS2YfZ0000'
│   ├── .key = 'input_data_imaging_usecase/images/Timepoint001_Row01_Well01_Alexa488_zstack001_r003_c005.tif'
│   ├── .size = 2333056
│   ├── .hash = '0aoXxT857VvKAGo9UQo-8g'
│   ├── .path = s3://lamin-eu-central-1/r7YUayXjktSb/.lamindb/Md4OouMExlWS2YfZ0000.tif
│   ├── .created_by = testuser1 (Test User1)
│   ├── .created_at = 2025-03-07 13:51:25
│   └── .transform = 'Transfer from `scportrait/examples`'
├── Linked features
│   └── FOV                         cat[ULabel]                FOV1                                     
│       cell_line_clone             cat[ULabel]                U2OS lcklip-mNeon mCherryLC3B clone 1    
│       channel                     cat[ULabel]                Alexa488                                 
│       genotype                    cat[ULabel]                WT                                       
│       imaged structure            cat[ULabel]                LckLip-mNeon                             
│       magnification               cat[ULabel]                20X                                      
│       microscope                  cat[ULabel]                Opera Phenix                             
│       stimulation                 cat[ULabel]                14h Torin-1                              
│       study                       cat[ULabel]                autophagy imaging                        
│       resolution                  float                      0.597976081                              
└── Labels
    └── .cell_lines                 bionty.CellLine            U-2 OS cell, U2OS                        
        .ulabels                    ULabel                     WT, 14h Torin-1, U2OS lcklip-mNeon mCher…

In addition, we create a Collection to hold all Artifact that belong to this specific imaging study.

collection = ln.Collection(
    artifacts,
    key="Annotated autophagy imaging raw images",
    description="annotated microscopy images of cells stained for autophagy markers",
).save()

Let’s look at some example images where we match images from the same clone, stimulation condition, and FOV to ensure correct channel alignment.

FOV_example_images = (
    metadata_files.sort_values(by=["cell_line_clone", "stimulation", "FOV"])
    .head(3)
    .reset_index(drop=True)
)

fig, axs = plt.subplots(1, 3, figsize=(15, 5))
for idx, row in FOV_example_images.iterrows():
    path = ln.Artifact.using("scportrait/examples").get(key=row["image_path"]).cache()
    image = imread(path)
    axs[idx].imshow(image)
    axs[idx].set_title(f"{row['imaged structure']}")
    axs[idx].axis("off")

FOV_example_images = (
    metadata_files.sort_values(by=["cell_line_clone", "stimulation", "FOV"])
    .tail(3)
    .reset_index(drop=True)
)

fig, axs = plt.subplots(1, 3, figsize=(15, 5))
for idx, row in FOV_example_images.iterrows():
    path = ln.Artifact.using("scportrait/examples").get(key=row["image_path"]).cache()
    image = imread(path)
    axs[idx].imshow(image)
    axs[idx].set_title(f"{row['imaged structure']}")
    axs[idx].axis("off")

→ mapped records: Artifact(uid='jVytS8AyAHmHkYR30000'), CellLine(uid='4oLoqaUP'), ULabel(uid='Aj8KGwbh'), ULabel(uid='A2945i5P'), ULabel(uid='JIbWVXma'), ULabel(uid='XKI9Mx33'), ULabel(uid='CrR7fgIZ'), ULabel(uid='QrU6fxsG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ mapped records: Artifact(uid='cw4F6bUB9zuMthCY0000'), CellLine(uid='4oLoqaUP'), ULabel(uid='HK8F1lVS'), ULabel(uid='Aj8KGwbh'), ULabel(uid='A2945i5P'), ULabel(uid='JIbWVXma'), ULabel(uid='CrR7fgIZ'), ULabel(uid='xhpmj7p7'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ mapped records: Artifact(uid='7TZGXvbA0JLL68hR0000'), CellLine(uid='4oLoqaUP'), ULabel(uid='Aj8KGwbh'), ULabel(uid='A2945i5P'), ULabel(uid='JIbWVXma'), ULabel(uid='AyafKoQw'), ULabel(uid='CrR7fgIZ'), ULabel(uid='xHqZKcIG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ mapped records: Artifact(uid='Ov8FnKzHMNY0XVJa0000'), CellLine(uid='4oLoqaUP'), ULabel(uid='9hHptuyb'), ULabel(uid='EgihgpJC'), ULabel(uid='GadMJgvN'), ULabel(uid='XKI9Mx33'), ULabel(uid='1KPobNqK'), ULabel(uid='QrU6fxsG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ mapped records: Artifact(uid='Lwk8shsYe0V5bMgd0000'), CellLine(uid='4oLoqaUP'), ULabel(uid='HK8F1lVS'), ULabel(uid='9hHptuyb'), ULabel(uid='EgihgpJC'), ULabel(uid='GadMJgvN'), ULabel(uid='1KPobNqK'), ULabel(uid='xhpmj7p7'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

→ mapped records: Artifact(uid='YuyVn060M4FxATPz0000'), CellLine(uid='4oLoqaUP'), ULabel(uid='9hHptuyb'), ULabel(uid='EgihgpJC'), ULabel(uid='GadMJgvN'), ULabel(uid='AyafKoQw'), ULabel(uid='1KPobNqK'), ULabel(uid='xHqZKcIG'), ULabel(uid='PKiCEP1h'), ULabel(uid='HRRTqARL'), ULabel(uid='e82fx2wm')

ln.finish()

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→ finished Run('4TQVxxtn') after 3m at 2025-06-03 16:34:29 UTC