Binding domain vocabulary for colony_tracking. These terms are used in
identifiers, help text, and documentation.
Sections: Data / Colonies / Exclusions-and-flags / Analysis.
plate — A 96-well culture plate; the unit of one experiment, one raw input tree, and one pipeline run.
well — One of the 96 wells of a plate, named like -A001 (the
-<A-H>\d{3} binding). In a flat
input tree the well is parsed from the leading -<A-H>\d{3} of the file
name; in a per-well input tree it is the subdirectory name. All stage
outputs are per-well nested subdirectories.
frame — One acquired image of a well. Frame metadata is parsed from the
file name in both input layouts: the frame number from LO<nnn>, the
acquisition time from the T field.
frame number — The 1-based index of a frame within a well, parsed from
LO<nnn> in the file name. Written to disk as frame.
reference frame — The frame all other frames of a well are differenced
against. Selected as first or by frame number (1-based).
time field — The T field of the file name, the acquisition time
(milliseconds in this dataset). Written to colonies.csv as t_seconds
(the raw value); converted to hours by the magnitude heuristic (values >
1e6 are read as milliseconds).
difference frame — cur − ref in counts for one well, stored as a uint8
preview with 128 = no change, scaled by the per-well display limit (ADR
0001).
display limit — The per-well ceiling that scales difference counts into
the uint8 preview: the display_percentile (99.5) of |diff|, estimated on
the subsampled grid. Recorded in the well's scale.txt as
display_limit_int16.
input tree layout — The two accepted layouts of stage inputs: flat (all wells' frames in one directory, the well parsed from the file name) and per-well (one subdirectory per well). All stage outputs are per-well nested subdirectories.
segment — One connected foreground region that the tracking rules consider. In a full segment run these are the instances that passed the growth-mask gating; in re-ID mode each saved label value is re-split into connected components.
instance — One connected foreground region the decoder fires on in a single frame (foreground above the stage's threshold).
group — One connected component of the union of the final frame's surviving instances. Groups are the units the growth mask is built from.
growth mask — The union of the final frame's groups, dilated by
mask_margin px. Detection in earlier frames is confined to it (ADR 0002).
colony — One tracked identity across frames: a series of one or more segments linked by the continue / merge / fork rules.
colony ID — The stable identity number of a colony. A surviving colony keeps its ID through merges and forks.
merge — Two or more colonies combining into one segment. The survivor
keeps its ID; the absorbed colonies are listed in merged_with.
absorbed — A colony that lost its identity in a merge. If it separates again it resumes its own ID.
fork — An unmatched segment that splits one colony: the same ID continues (logged and counted in the done marker).
pre-existing — A colony whose first detection is at or before the
exclude_before frame, or that is probed pre-existing against the raw root
(or, without one, against the raw reference frame itself) for a difference
root. Flagged pre_existing=1; excluded from aggregates and plots over its
whole lifetime unless keep_pre_existing, and never bad-flagged (so it
cannot exclude its well).
well circle — The fitted meniscus circle of a well (well, cy, cx, R
in well_geometry.csv), the anchor of rim exclusion.
rim — The band within rim_width_px of the well circle.
rim-excluded — A colony, from the first frame in which more than
rim_overlap_max of its pixels lie in the rim. Exclusion is monotone:
colonies only grow into the rim.
bad segment — A colony flagged from_start (first valid frame within
start_frames of the series start) or no_growth (any valid frame,
compared to the earliest valid frame ≥ 2 images ahead, growing by
min_growth_per_frame or less per image).
bad well — A well with ≥ max_bad_segments distinct bad colonies;
excluded from aggregates and plots unless keep_bad_wells.
ancestors — The transitive, self-inclusive count of the original
colonies combined in a segment (1 = unmerged; an A+B where B had merged
with C ends at 3). Written as ancestors (the prototype's n_merged).
drift gate — The skip of a frame whose elevated-foreground fraction
exceeds max(max_fg_ratio × reference-frame fraction, 0.05); drift bursts
around the reference frame make the decoder hallucinate giant instances.
max_fg_ratio = 0 disables the gate (ADR 0002).
exclude_before — A frame number N that flags colonies first detected at or before N as pre-existing; frames before N are segmented and tracked like any other (nothing is blanked).
growth rate — The per-colony rates over its valid (not rim-excluded)
frames, computed only when the window is at least three frames wide
(first to last valid frame ≥ 2 images apart — the same window the
per-frame no_growth comparison needs; a bare two-point slope cannot be
vetted against the growth floor): the exponential rate (least-squares
slope of ln(area) vs hours, and doublings per day) and the absolute
growth (px/h). Narrower-window colonies (single valid frame, two adjacent
frames) get blank rate cells and are skipped by the pooled aggregates and
plots.
pooled — Cross-well statistics grouped by ancestor count: pooled area statistics per (frame, ancestors) and pooled rate statistics per max-ancestors.