Description

This plugin allows to open particle tracking results from multiple formats into the Napari Tracks Layer.

Supported formats

The formats currently supported by this plugin are:

CSV

The most basic format to store particle tracking tracks is a CSV file containing the tracks table. In this format each line is a particle and each column a property of the particle. The table headers must be TrackID, t, x, y, z. Note that the header order does not matter:

CSV structure example

TrackID	t	x	y	z
0	16	41.5828343348868	47.505930020081664	0
0	17	41.48425270538317	51.6023835597057	0

The raw CSV file is a classical comma-separated values format:

TrackID,t,x,y,z
0,16, 41.5828343348868, 47.505930020081664, 0
0,17, 41.48425270538317, 51.6023835597057, 0
...

Warning

This CSV format does not support split and merge events

TrackMate

The TrackMate format is the XML model file générated by the [TrackMate](https://imagej.net/plugins/trackmate/) Fiji plugin. The XML file from TrackMate should not be manually modified and and contains a Model element:

<?xml version="1.0" encoding="UTF-8"?>
<TrackMate version="6.0.2">
...
<Model spatialunits="pixel" timeunits="sec">
    <FeatureDeclarations>
      <SpotFeatures>
        <Feature feature="QUALITY" name="Quality" shortname="Quality" dimension="QUALITY" isint="false" />
        <Feature feature="POSITION_X" name="X" shortname="X" dimension="POSITION" isint="false" />
...

All the particles features from the TrackMate model file are loaded in the napari tracks properties.

Note

This format supports split and merge events

Icy

The Icy format is a XML file generated by the [Icy](http://icy.bioimageanalysis.org/plugin/spot-tracking/) software. The XML file from ICY should not be manually modified and starts with the root element:

<?xml version="1.0" encoding="UTF-8"?>
<root>
  <trackfile version="1" />
  <trackgroup>
    <track id="265713726">
      <detection t="16" x="41.5828343348868" y="47.505930020081664" z="0" classname="plugins.nchenouard.particleTracking.sequenceGenerator.ProfileSpotTrack" type="1" />
      <detection t="17" x="41.48425270538317" y="51.6023835597057" z="0" classname="plugins.nchenouard.particleTracking.sequenceGenerator.ProfileSpotTrack" type="1" />
      ...

Note

This format supports split and merge events

ISBI

The ISBI format is a XML format used for the ISBI tracking challenge. This format must contain a root element and a list of particles in a TrackContestISBI2012 element:

<?xml version="1.0" encoding="UTF-8"?>
<root>
  <TrackContestISBI2012 snr="?" density="?" scenario="FakeTracks.tif" generationDateTime="Wed May 12 14:07:09 CEST 2021">
    <particle>
      <detection t="0" x="64.00558680057657" y="3.9587411612103076" z="0.0" />
      <detection t="1" x="63.98171495578894" y="6.04150382894106" z="0.0" />
      <detection t="2" x="63.95406806092088" y="10.06085170348766" z="0.0" />

Warning

This format does not support split and merge events

Quickstart

You can open local tracks using napari at the terminal and the path to your file:

napari /path/to/your/tracks.xml

OR in python:

import napari

viewer = napari.Viewer()
viewer.open('/path/to/your/tracks.xml')
napari.run()

Getting Help

If you discover a bug with the plugin, or would like to request a new feature, please raise an issue on our repository at https://github.com/sylvainprigent/napari-tracks-reader.