The images used here were acquired as part of a study (Publication) on autophagy, a cellular process during which cells recycle their components in autophagosomes. To identify genetic determinants of autophagy, the study tracked the formation of autophagosomes through microscopy of the fluorescent autophagosome marker mCherry-LC3B following treatment of cells with the autophagy inducer Torin-1.

Here, we ingest the microscopy data, consisting of TIFF image stacks and the corresponding metadata file - a standard format for such imaging experiments.

import lamindb as ln
import pandas as pd
import tifffile
import matplotlib.pyplot as plt

ln.track()

assert ln.setup.settings.instance.slug == "scportrait/examples"

→ connected lamindb: scportrait/examples
→ created Transform('fl9HcsEgLIr70000'), started new Run('JS8hDOb2...') at 2025-03-07 13:51:21 UTC
→ notebook imports: lamindb==1.1.1 matplotlib==3.10.0 pandas==2.2.3 tifffile==2025.2.18

# The metadata file contains the file paths of the images and all associated metadata
# We can load it later to annotate the imaging data
metadata = pd.read_csv("input_data_imaging_usecase/metadata_files.csv")
metadata.head(3)
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
2 input_data_imaging_usecase/images/Timepoint001... WT 14h Torin-1 U2OS U2OS lcklip-mNeon mCherryLC3B clone 1 DAPI FOV1 20X Opera Phenix DNA 0.597976 
# An example image
img = tifffile.imread(metadata.iloc[0]["image_path"])
plt.imshow(img)
plt.axis("off")
plt.show()
No description has been provided for this image 
# Ingest the imaging data directory, using the image_path prefix as the key
# This ensures that the image_path and loaded Artifact paths still align
artifacts = ln.Artifact.from_dir(
    "./input_data_imaging_usecase", key="input_data_imaging_usecase"
)
ln.save(artifacts)

... uploading metadata_files.csv: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/metadata_files.csv already exists, replacing it.
... uploading config.yml: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/config.yml already exists, replacing it.
... uploading Timepoint001_Row03_Well01_Alexa488_zstack001_r001_c008.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row03_Well01_Alexa488_zstack001_r001_c008.tif already exists, replacing it.
... uploading Timepoint001_Row01_Well08_Alexa488_zstack001_r002_c009.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row01_Well08_Alexa488_zstack001_r002_c009.tif already exists, replacing it.
... uploading Timepoint001_Row04_Well01_mCherry_zstack001_r001_c002.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row04_Well01_mCherry_zstack001_r001_c002.tif already exists, replacing it.
... uploading Timepoint001_Row01_Well01_Alexa488_zstack001_r004_c007.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row01_Well01_Alexa488_zstack001_r004_c007.tif already exists, replacing it.
... uploading Timepoint001_Row04_Well08_Alexa488_zstack001_r001_c003.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row04_Well08_Alexa488_zstack001_r001_c003.tif already exists, replacing it.
... uploading Timepoint001_Row01_Well08_DAPI_zstack001_r002_c010.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row01_Well08_DAPI_zstack001_r002_c010.tif already exists, replacing it.
... uploading Timepoint001_Row03_Well01_mCherry_zstack001_r001_c008.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row03_Well01_mCherry_zstack001_r001_c008.tif already exists, replacing it.
... uploading Timepoint001_Row02_Well08_Alexa488_zstack001_r002_c009.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row02_Well08_Alexa488_zstack001_r002_c009.tif already exists, replacing it.
... uploading Timepoint001_Row02_Well01_DAPI_zstack001_r005_c008.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row02_Well01_DAPI_zstack001_r005_c008.tif already exists, replacing it.
... uploading Timepoint001_Row04_Well08_Alexa488_zstack001_r001_c005.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row04_Well08_Alexa488_zstack001_r001_c005.tif already exists, replacing it.
... uploading Timepoint001_Row02_Well08_DAPI_zstack001_r002_c005.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row02_Well08_DAPI_zstack001_r002_c005.tif already exists, replacing it.
... uploading Timepoint001_Row02_Well01_mCherry_zstack001_r005_c008.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row02_Well01_mCherry_zstack001_r005_c008.tif already exists, replacing it.
... uploading Timepoint001_Row03_Well08_Alexa488_zstack001_r010_c010.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row03_Well08_Alexa488_zstack001_r010_c010.tif already exists, replacing it.
... uploading Timepoint001_Row03_Well08_DAPI_zstack001_r010_c010.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row03_Well08_DAPI_zstack001_r010_c010.tif already exists, replacing it.
... uploading Timepoint001_Row01_Well08_mCherry_zstack001_r002_c010.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row01_Well08_mCherry_zstack001_r002_c010.tif already exists, replacing it.
... uploading Timepoint001_Row02_Well01_mCherry_zstack001_r008_c008.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row02_Well01_mCherry_zstack001_r008_c008.tif already exists, replacing it.
... uploading Timepoint001_Row03_Well08_mCherry_zstack001_r010_c010.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row03_Well08_mCherry_zstack001_r010_c010.tif already exists, replacing it.
... uploading Timepoint001_Row04_Well01_Alexa488_zstack001_r001_c009.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row04_Well01_Alexa488_zstack001_r001_c009.tif already exists, replacing it.
... uploading Timepoint001_Row02_Well08_mCherry_zstack001_r002_c005.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row02_Well08_mCherry_zstack001_r002_c005.tif already exists, replacing it.
... uploading Timepoint001_Row02_Well01_DAPI_zstack001_r008_c008.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row02_Well01_DAPI_zstack001_r008_c008.tif already exists, replacing it.
... uploading Timepoint001_Row04_Well01_DAPI_zstack001_r001_c002.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row04_Well01_DAPI_zstack001_r001_c002.tif already exists, replacing it.
... uploading Timepoint001_Row01_Well01_Alexa488_zstack001_r003_c005.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row01_Well01_Alexa488_zstack001_r003_c005.tif already exists, replacing it.
... uploading Timepoint001_Row03_Well01_DAPI_zstack001_r001_c008.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row03_Well01_DAPI_zstack001_r001_c008.tif already exists, replacing it.
... uploading Timepoint001_Row04_Well01_Alexa488_zstack001_r001_c002.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row04_Well01_Alexa488_zstack001_r001_c002.tif already exists, replacing it.
... uploading Timepoint001_Row01_Well01_DAPI_zstack001_r003_c005.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row01_Well01_DAPI_zstack001_r003_c005.tif already exists, replacing it.
... uploading Timepoint001_Row03_Well01_DAPI_zstack001_r001_c007.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row03_Well01_DAPI_zstack001_r001_c007.tif already exists, replacing it.
... uploading Timepoint001_Row03_Well08_mCherry_zstack001_r010_c009.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row03_Well08_mCherry_zstack001_r010_c009.tif already exists, replacing it.
... uploading Timepoint001_Row02_Well08_mCherry_zstack001_r002_c009.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row02_Well08_mCherry_zstack001_r002_c009.tif already exists, replacing it.
... uploading Timepoint001_Row04_Well01_DAPI_zstack001_r001_c009.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row04_Well01_DAPI_zstack001_r001_c009.tif already exists, replacing it.
... uploading Timepoint001_Row01_Well08_mCherry_zstack001_r002_c009.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row01_Well08_mCherry_zstack001_r002_c009.tif already exists, replacing it.
... uploading Timepoint001_Row02_Well01_Alexa488_zstack001_r008_c008.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row02_Well01_Alexa488_zstack001_r008_c008.tif already exists, replacing it.
... uploading Timepoint001_Row03_Well08_DAPI_zstack001_r010_c009.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row03_Well08_DAPI_zstack001_r010_c009.tif already exists, replacing it.
... uploading Timepoint001_Row01_Well01_mCherry_zstack001_r003_c005.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row01_Well01_mCherry_zstack001_r003_c005.tif already exists, replacing it.
... uploading Timepoint001_Row04_Well08_DAPI_zstack001_r001_c005.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row04_Well08_DAPI_zstack001_r001_c005.tif already exists, replacing it.
... uploading Timepoint001_Row01_Well01_mCherry_zstack001_r004_c007.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row01_Well01_mCherry_zstack001_r004_c007.tif already exists, replacing it.
... uploading Timepoint001_Row03_Well08_Alexa488_zstack001_r010_c009.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row03_Well08_Alexa488_zstack001_r010_c009.tif already exists, replacing it.
... uploading Timepoint001_Row02_Well08_DAPI_zstack001_r002_c009.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row02_Well08_DAPI_zstack001_r002_c009.tif already exists, replacing it.
... uploading Timepoint001_Row02_Well01_Alexa488_zstack001_r005_c008.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row02_Well01_Alexa488_zstack001_r005_c008.tif already exists, replacing it.
... uploading Timepoint001_Row04_Well01_mCherry_zstack001_r001_c009.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row04_Well01_mCherry_zstack001_r001_c009.tif already exists, replacing it.
... uploading Timepoint001_Row02_Well08_Alexa488_zstack001_r002_c005.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row02_Well08_Alexa488_zstack001_r002_c005.tif already exists, replacing it.
... uploading Timepoint001_Row04_Well08_mCherry_zstack001_r001_c005.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row04_Well08_mCherry_zstack001_r001_c005.tif already exists, replacing it.
... uploading Timepoint001_Row03_Well01_Alexa488_zstack001_r001_c007.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row03_Well01_Alexa488_zstack001_r001_c007.tif already exists, replacing it.
... uploading Timepoint001_Row04_Well08_DAPI_zstack001_r001_c003.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row04_Well08_DAPI_zstack001_r001_c003.tif already exists, replacing it.
... uploading Timepoint001_Row01_Well08_DAPI_zstack001_r002_c009.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row01_Well08_DAPI_zstack001_r002_c009.tif already exists, replacing it.
... uploading Timepoint001_Row01_Well01_DAPI_zstack001_r004_c007.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row01_Well01_DAPI_zstack001_r004_c007.tif already exists, replacing it.
... uploading Timepoint001_Row01_Well08_Alexa488_zstack001_r002_c010.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row01_Well08_Alexa488_zstack001_r002_c010.tif already exists, replacing it.
... uploading Timepoint001_Row04_Well08_mCherry_zstack001_r001_c003.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row04_Well08_mCherry_zstack001_r001_c003.tif already exists, replacing it.
... uploading Timepoint001_Row03_Well01_mCherry_zstack001_r001_c007.tif: 100.0%
! The cache path /Users/sophia/Library/Caches/lamindb/lamin-eu-central-1/r7YUayXjktSb/input_data_imaging_usecase/images/Timepoint001_Row03_Well01_mCherry_zstack001_r001_c007.tif already exists, replacing it.

ln.Collection(
    artifacts,
    key="input_data_imaging_usecase",
    description="TIFF stacks and metadata of mCherry-LC3B microscopy.",
).save()

Collection(uid='Rmih9GYkxu7XkfJb0000', is_latest=True, key='input_data_imaging_usecase', description='TIFF stacks and metadata of mCherry-LC3B microscopy.', hash='eTH09h0RFo1pKdh0MRcD8Q', created_by_id=4, space_id=1, run_id=674, created_at=2025-03-07 13:51:39 UTC)
ln.finish()