sc-imaging¶
Here, you will learn how to structure, featurize, and make a large imaging collection queryable for large-scale machine learning:
Load and annotate a
Collectionof microscopy images (Generate single-cell images (
)
Featurize single-cell images (
)
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
Show code cell output
→ 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()
Show code cell output
→ connected lamindb: testuser1/test-sc-imaging
→ created Transform('IwdzSGgDJ8DX0000'), started new Run('lVfelBPF...') at 2025-04-22 18:35:57 UTC
→ notebook imports: bionty==1.3.0 lamindb==1.4.0 matplotlib==3.10.1 tifffile==2025.3.30
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)
Show code cell output
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ completing transfer to track Artifact('jdjwcUB0') as input
→ mapped records:
→ 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())
Show code cell output
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)
Show code cell output
! 2 terms are not validated: 'WT', 'EI24KO'
→ fix typos, remove non-existent values, or save terms via .add_new_from("genotype")
! 2 terms are not validated: '14h Torin-1', 'untreated'
→ fix typos, remove non-existent values, or save terms via .add_new_from("stimulation")
! 1 term is not validated: 'U2OS'
1 synonym found: "U2OS" → "U-2 OS cell"
→ curate synonyms via .standardize("cell_line")
! 4 terms are not validated: '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 .add_new_from("cell_line_clone")
! 3 terms are not validated: 'Alexa488', 'DAPI', 'mCherry'
→ fix typos, remove non-existent values, or save terms via .add_new_from("channel")
! 2 terms are not validated: 'FOV1', 'FOV2'
→ fix typos, remove non-existent values, or save terms via .add_new_from("FOV")
! 1 term is not validated: '20X'
→ fix typos, remove non-existent values, or save terms via .add_new_from("magnification")
! 1 term is not validated: 'Opera Phenix'
→ fix typos, remove non-existent values, or save terms via .add_new_from("microscope")
! 3 terms are not validated: 'LckLip-mNeon', 'DNA', 'mCherry-LC3B'
→ fix typos, remove non-existent values, or save terms via .add_new_from("imaged structure")
Add and standardize missing terms:
curator.cat.standardize("cell_line")
curator.cat.add_new_from("all")
curator.validate()
Show code cell output
! '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_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||
| 5 | uSzt6lqi | U2OS lcklip-mNeon mCherryLC3B clone 1 | False | None | None | None | 1 | None | 1 | 2025-04-22 18:36:10.449000+00:00 | 1 | None | 1 |
| 6 | 7lhk0KXx | U2OS lcklip-mNeon mCherryLC3B clone 2 | False | None | None | None | 1 | None | 1 | 2025-04-22 18:36:10.449000+00:00 | 1 | None | 1 |
| 7 | O8dnwfF0 | U2OS lcklip-mNeon mCherryLC3B EI24 KO clone 1 | False | None | None | None | 1 | None | 1 | 2025-04-22 18:36:10.449000+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_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||
| 5 | uSzt6lqi | U2OS lcklip-mNeon mCherryLC3B clone 1 | False | None | None | None | 1 | None | 1 | 2025-04-22 18:36:10.449000+00:00 | 1 | None | 1 |
| 6 | 7lhk0KXx | U2OS lcklip-mNeon mCherryLC3B clone 2 | False | None | None | None | 1 | None | 1 | 2025-04-22 18:36:10.449000+00:00 | 1 | None | 1 |
| 7 | O8dnwfF0 | U2OS lcklip-mNeon mCherryLC3B EI24 KO clone 1 | False | None | None | None | 1 | None | 1 | 2025-04-22 18:36:10.449000+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)
Show code cell output
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ mapped records:
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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')
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ 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.name] FOV1 │ cell_line_clone cat[ULabel.name] U2OS lcklip-mNeon mCherryLC3B clone 1 │ channel cat[ULabel.name] Alexa488 │ genotype cat[ULabel.name] WT │ imaged structure cat[ULabel.name] LckLip-mNeon │ magnification cat[ULabel.name] 20X │ microscope cat[ULabel.name] Opera Phenix │ stimulation cat[ULabel.name] 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")
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ completing transfer to track Artifact('jVytS8Ay') as input
→ 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')
→ transferred records:
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ completing transfer to track Artifact('cw4F6bUB') as input
→ 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')
→ transferred records:
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ completing transfer to track Artifact('7TZGXvbA') as input
→ 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')
→ transferred records:
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ completing transfer to track Artifact('Ov8FnKzH') as input
→ 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')
→ transferred records:
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ completing transfer to track Artifact('Lwk8shsY') as input
→ 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')
→ transferred records:
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
! source modules has additional modules: set()
consider mounting these registry modules to transfer all metadata
→ completing transfer to track Artifact('YuyVn060') as input
→ 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')
→ transferred records:
ln.finish()
Show code cell output
→ finished Run('lVfelBPF') after 7m at 2025-04-22 18:43:01 UTC