Result files

What tracell track, tracell live and the app's export write. The same list is in the program: tracell reference files and tracell reference columns (add --format json for scripts).

A recorded video: tracell track

File	What
NAME_tracks.csv	One row per cell per frame (columns: tracks). .xlsx/.txt with --format.
NAME_cells.csv	One row per cell (columns: cells).
NAME_settings.json	The preset that was used; File > Load and --preset read it.
NAME_traces.mp4	With --video-out: the video with the tracks drawn in.

A live session: tracell live (the session folder)

File	What
session.json	What ran and one entry per partition (keys below). Rewritten after every partition.
tables/partition_NNNN.csv	One row per cell per frame of that partition (columns: tracks + live).
cells.csv	One row per cell of every partition, appended after each partition (columns: cells + live).
crops/partition_NNNN.npz	With --crops: arrays with_background and/or without_background (rows, size, size) uint8, plus partition, particle_id, frame per row.
video/	With --record: the raw frames of each partition (AVI).

tracell track names the files after the video (or --name). A session folder is named by date and time and never reused. Its files are written while the session runs, so another program can read them as it goes: read session.json first and only the tables it lists.

session.json

Key	Meaning
started	ISO time the session started.
ended	ISO time it ended; null while it runs (or when it was killed).
fps	Frame rate of the camera.
crops	Crop mode (none, with_background, without_background, both).
crop_size	Crop side in pixels.
settings	The preset the session ran with.
partitions	One entry per partition, in order:
partitions[].partition	Partition number, from 1.
partitions[].frames	Frames in it.
partitions[].source_first_frame	With a virtual camera: the video frame it started at.
partitions[].finished_at	ISO time it was tracked.
partitions[].points	Rows in its table.
partitions[].cells	Cells in it.
partitions[].complete_cells	Complete cells in it.
partitions[].table	Its table, relative to the folder (null when nothing was tracked).
partitions[].crops	Its crops file, or null.
partitions[].features	With features: pending, done or failed.
partitions[].feature_columns	With features: the columns that were added.

Columns

Coordinates and sizes are in pixels of the processed picture (after the ROI and the scale). With a calibration every length, area and speed column also comes in µm, µm² and µm/s, and frame columns in seconds.

Column	Unit	Tables	Meaning
partition		live tracks, live cells	Live partition the row belongs to (from 1). Frame numbers and cell IDs restart in each.
particle_id		tracks, cells	Cell ID. Unique within a video, or within a partition. IDs are not stable between runs; compare tracks, not IDs.
frame	frames	tracks	Frame number in the video, or in the partition.
x	pixels	tracks	Center of the cell, x (of the processed picture: after ROI and scale).
y	pixels	tracks	Center of the cell, y.
area	pixels²	tracks	Area of the cell's contour.
perimeter	pixels	tracks	Perimeter of the contour.
eq_diameter	pixels	tracks	Diameter of a circle with the same area.
circularity		tracks	4πA/p²: 1 for a circle, lower for other shapes.
complete		live tracks, live cells	true when the track is not cut at the partition's start or end and is long enough (min_track_share). Counts and stop goals use only complete cells.
time_s	s	live tracks	Time of the frame since the session started.
crop		live tracks (with crops)	Row of this point's crop in crops/partition_NNNN.npz.
first_frame	frames	cells	First frame the cell was seen.
last_frame	frames	cells	Last frame the cell was seen.
points	frames	cells	Frames the cell was detected in (track length).
missing_frames	frames	cells	Frames between first and last where it was not detected.
x_first	pixels	cells	x where it was first seen.
y_first	pixels	cells	y where it was first seen.
x_last	pixels	cells	x where it was last seen.
y_last	pixels	cells	y where it was last seen.
displacement	pixels	cells	Straight distance from first to last position.
path_length	pixels	cells	Length of the path along the track.
speed_mean	pixels per frame	cells	path_length / (last_frame - first_frame).
area_mean	pixels²	cells	Mean area over the track; area_std its standard deviation.
perimeter_mean	pixels	cells	Mean perimeter; perimeter_std its standard deviation.
eq_diameter_mean	pixels	cells	Mean equivalent diameter; eq_diameter_std its standard deviation.
circularity_mean		cells	Mean circularity; circularity_std its standard deviation.
duration_s	s	cells	Time from first to last frame (needs the frame rate).
*_um, *_um2, *_um_s	µm, µm², µm/s	tracks, cells	With a calibration (model.region.pixel_size_um, frame_rate): the same value as the pixel column of that name, in micrometers and seconds.
<feature> / <feature>_mean		live tracks, live cells	Measurements of model.live.features (e.g. dn_* from an External server): per point in the partition tables, per-cell mean in cells.csv.