TrackMate CSV Importer¶

The TrackMate CSV Importer is a Fiji plugin that loads pre-computed spot/detection tables (CSV format) directly into TrackMate, skipping the detection step. This is the key integration point between pyCyto’s segmentation/tabulation outputs and TrackMate tracking.

Plugin page: https://imagej.net/plugins/trackmate/extensions/csv-importer

Why This Matters¶

pyCyto’s standard pipeline produces a per-cell features DataFrame (from cyto.tabulation) that contains cell centroids, sizes, and intensities per frame. Without the CSV Importer, you would have to re-run TrackMate’s built-in detection on the raw images. With the plugin, you pass the DataFrame directly — TrackMate skips detection and goes straight to tracking.

Installation¶

Auto-download mode (PyImageJ)¶

When using imagej.init('sc.fiji:fiji'), the CSV Importer is included in the default Fiji update site and is available automatically.

Pre-installed Fiji¶

/path/to/Fiji.app/ImageJ-linux64 --headless --ij2 --update \
    add-update-site TrackMateCSVImporter \
    https://sites.imagej.net/TrackMateCSVImporter/
/path/to/Fiji.app/ImageJ-linux64 --headless --ij2 --update update

CSV Format¶

The importer expects a CSV with at minimum these columns (matching TrackMate spot attributes):

Column	TrackMate attribute	Notes
`x`	`POSITION_X`	pixel or physical units
`y`	`POSITION_Y`	pixel or physical units
`frame`	`FRAME`	0-based integer
`feret_radius`	`RADIUS`	estimated cell radius
`mean`	`QUALITY`	mean intensity, used for quality

pyCyto’s tabulation output (data["dataframe"]) already has these columns. The cyto.tracking.trackmate wrapper handles the column mapping automatically.

Python API¶

from cyto.tracking.trackmate import TrackMateInMemoryProcessor

tracker = TrackMateInMemoryProcessor(
    fiji_dir="",          # "" = auto-download
    verbose=True,
)

result = tracker({
    "label": label_array,   # OR
    "features": spots_df,   # pre-computed spot DataFrame
})

tracks_df = result["features"]

Scripting with scyjava¶

For advanced use, you can call the CSV Importer Java API directly:

import scyjava
CSVImporter = scyjava.jimport(
    'fiji.plugin.trackmate.io.TmXmlWriter'
)

See trackmate_in_mem.md for the full in-memory TrackMate workflow.