From da62c5e87eb48ac2c5a63783e87a8b18d4ca1705 Mon Sep 17 00:00:00 2001
From: Krzysztof Gonciarz <gonciarz@mpi-cbg.de>
Date: Fri, 20 Oct 2023 09:54:29 +0200
Subject: [PATCH] Added info about running PT from macro (MSS, absolute value)
---
doc/source/particleTrackerTutorial.rst | 18 ++++++++++++++++++
1 file changed, 18 insertions(+)
diff --git a/doc/source/particleTrackerTutorial.rst b/doc/source/particleTrackerTutorial.rst
index d5f18104..74fc1415 100644
--- a/doc/source/particleTrackerTutorial.rst
+++ b/doc/source/particleTrackerTutorial.rst
@@ -375,6 +375,24 @@ The expected columns are only: Frame, x, y, z. Optionally provided columns m0 an
Macros
======
+How to run Particle Tracker from ImageJ macro
+---------------------------------------------
+
+Here are examples of run commands for Particle Tracker
+
+.. code-block:: guess
+
+ run("Particle Tracker 2D/3D", "radius=3 cutoff=0.001 per/abs=0.501 link=2 displacement=10 dynamics=Brownian");
+ run("Particle Tracker 2D/3D", "radius=3 cutoff=0.001 per/abs=0.500 link=2 displacement=10 dynamics=Brownian saveMss");
+ run("Particle Tracker 2D/3D", "radius=3 cutoff=0.001 per/abs=50 absolute link=2 displacement=10 dynamics=Brownian");
+
+While most parameters is self describing (same names as in Particle Trakcer dialog) here are exceptions:
+
+1. **absolute** - add this argument to have 'Absolute' cutoff rather than percentile ('Absolute' checkbox)
+#. **saveMss** - add this argument to save MSS to file (table that is accessible via "All MSS/MSD to Table' in GUI mode)
+
+After running in macro mode ParticleTracker will save output files in same directory as input image file.
+
Postprocess "All Trajectories to Table"
---------------------------------------
--
GitLab