Lineage and Cells#

Source | API

The lineage module contains three essential classes: delta.lineage.Lineage, which is a collection of delta.lineage.Cell s, themselves composed of delta.lineage.CellFeatures.

The purpose of delta.lineage.Lineage is to store cell features (length, area, average fluorescence, etc.) and their lineage tree (who divided into who). For example, let’s load a position from the DeLTA test suite and see what the lineage looks like:

# Load the position
pos = delta.pipeline.Position.load_netcdf(
    "tests/data/movie_2D_nd2/test_expected_results/Position000000.nc"
)
# Take the lineage from the first (and only) ROI
lineage = pos.rois[0].lineage
# Print it
print(lineage)

frames    : ..........
cell #0001: ╺╼╼╼╼╼┮╼╼╼
cell #0002:       ┕╼╼╼

This compact representation of the lineage shows that there was one cell that divided into two after a few frames.

The two cells can be found in the cells dictionary of the lineage, under their cell ids. Let’s look at them in more detail:

mother = lineage.cells[1]
daughter = lineage.cells[2]

These objects are delta.lineage.Cell objects. They can be queried for information as following:

# The mother has no mother, but the daughter does
assert mother.motherid is None
assert daughter.motherid == 1

# The daughter appeared on frame 6
assert daughter.first_frame == 6

# Let's check this information also from the mother's side
assert mother.daughterid(frame=5) is None
assert mother.daughterid(frame=6) == 2
assert mother.daughterid(frame=7) is None

Finally, the method features returns an object containing all the morphological features of the cell at a given frame:

print(mother.features(frame=4))

CellFeatures(
    new_pole=array([260, 341], dtype=int16),
    old_pole=array([260, 370], dtype=int16),
    length=37.0,
    width=7.0,
    area=200.5,
    perimeter=82.38477,
    fluo=array([], dtype=float32),
    edges='',
    growthrate_length=0.084183276,
    growthrate_area=0.06813244,
)

Note

A detailed description of the individual features, their signification and units, is available in the documentation page of delta.lineage.CellFeatures.

Individual features can be accessed by fields:

assert mother.features(frame=4).area == 200.5

The delta.lineage.Lineage class contains several methods that allow to manipulate the lineage in case of tracking errors. They are described in the documentation page for delta.lineage.Lineage.