Bug 1160 – Threshold value in Trackmate is not stricktly used while tracking particles. most of the time particles considered in tracking analysis have intensity values much lower than the threshold value set before starting the analysis.

Bug 1160 - Threshold value in Trackmate is not stricktly used while tracking particles. most of the time particles considered in tracking analysis have intensity values much lower than the threshold value set before starting the analysis.


Summary:	Threshold value in Trackmate is not stricktly used while tracking particles. ...

Status:	RESOLVED FIXED

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	PC Windows

Importance:	P4 normal
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2015-09-16 04:21 CDT by Deepika Sharma
Modified:	2015-10-21 07:02 CDT
CC List:	4 users (show)

See Also:

Attachments
TrackMate spot filter on 'Maximum intensity' (28.04 KB, image/png) 2015-10-21 07:02 CDT, Jan Eglinger

Description Deepika Sharma 2015-09-16 04:21:21 CDT

Trackmate.
Threshold value is not used stricktly during the tracking of particles. 
Problematic when user requires specific particles to track.

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Tools\FID6A6~1.APP/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Tools\FID6A6~1.APP

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150915154157)
Fiji: http://update.fiji.sc/ (last check:20150910233236)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20150912032644)
BioVoxxel: http://sites.imagej.net/BioVoxxel/ (last check:20150819111801)
HDF5: http://sites.imagej.net/Ronneber/ (last check:20150214134119)
IBMP-CNRS: http://www-ibmp.u-strasbg.fr/fijiupdates/ (last check:20150318110643)
IMCF Uni Basel: http://sites.imagej.net/UniBas-IMCF/ (last check:20150628195511)
LOCI: http://sites.imagej.net/LOCI/ (last check:20150428235912)
Ehrenfeu: http://sites.imagej.net/Ehrenfeu/ (last check:20150127151701)

Files not up-to-date:
  53318765 (UPDATEABLE) 20150914131925 jars/imagej-2.0.0-rc-38.jar
  2775ecd7 (UPDATEABLE) 20150914131926 jars/imagej-plugins-commands-0.5.2.jar
  94d7c287 (UPDATEABLE) 20150914131927 jars/imagej-ui-swing-0.14.0.jar
  ef093e5d (UPDATEABLE) 20150628195950 jars/rsyntaxtextarea-2.5.6.jar
  1dbc6331 (LOCAL_ONLY) 20150603213848 plugins/Imaris/ImarisBridgeUtils.jar
  eb679ca0 (LOCAL_ONLY) 20150603213848 plugins/Imaris/Imaris_Bridge81.jar

Comment 1 Curtis Rueden 2015-10-13 11:09:40 CDT

Migrated to TrackMate GitHub issues, to increase visibility of this bug:
  https://github.com/fiji/TrackMate/issues/69

Comment 2 Jean-Yves Tinevez 2015-10-18 10:29:16 CDT

Hi Deepika

I can not confirm the bug your report. In my tests, the thresholds are respected. But I may have missed something.

Could you elaborate on this bug and give me a way to reproduce it?

Comment 3 Jean-Yves Tinevez 2015-10-21 04:00:20 CDT

Hi Deepika
I close this bug as invalid. If the problem reappears please contact me with a way to reproduce the bug.

Comment 4 Deepika Sharma 2015-10-21 04:15:21 CDT

Hi Jean, 

Could you please tell me how can I send you a ~200MB file that I am using for particle tracking. so that you can reproduce the bug. 

Thank you. 

Regards
Deepika 

(In reply to Jean-Yves Tinevez from comment #3)
> Hi Deepika
> I close this bug as invalid. If the problem reappears please contact me with
> a way to reproduce the bug.

Comment 5 Jean-Yves Tinevez 2015-10-21 05:56:42 CDT

Hi Deepika,

You can use Pasteur transfer service:
http://dl.pasteur.fr/index.html

Comment 6 Deepika Sharma 2015-10-21 06:40:08 CDT

Hi Jean,

Please find the file : http://dl.pasteur.fr/fop/vYsEyEDz/09.09.2015_60XOil_30uM_Impb_SYbeads_20fps_20ms_20instensity_561nm_14-1.tif

Please use following values at consecutive steps for TrackMate based particle analysis:
1- detector : LoG detector
2- blob diameter: 1um; Threshold: 65000.0
3- Select View: HyperStack Displayer
4- Set filters on spots: Set color by = Maximal intensity 
5- LAP Tracker 
6- Frame to frame linking: Max distance = 1.0 um (other options are unchecked)
7- Set filters on tracks: Track index
8- zoom in the track and observe the circle around the moving particle, you will see not all particle has intensity = 65000. 

In my case I need only particle with intensity equal or higher than the threshold values. So it would be great if you could tell me some way of achieving that from Trackmate.

Comment 7 Jean-Yves Tinevez 2015-10-21 06:59:25 CDT

Hi Deepika

Thank you I received the file and could play with it.

There is a major misunderstanding here, and it is caused by outdated documentation. 

Indeed, the threshold you set in the LoG detector panel is NOT a threshold on spot maximal intensity, but on spot QUALITY. The spot quality is a value generated by detectors that has no direct link with maximal intensity. It simple reflects how certain is the detector that the spot it finds is a good one. 

However, I read the documentation again, and it states that the threshold indeed acts on maximal intensity, which is wrong. See 
http://fiji.sc/Getting_started_with_TrackMate

I will fix this. 

Now if you want to filter spot on maximal intensity, you have to use a filter on this value in the spot filter panel.

Thank you very much.

Comment 8 Jan Eglinger 2015-10-21 07:02:58 CDT

Created attachment 270
TrackMate spot filter on 'Maximum intensity'

The threshold during spot detection works on the 'Quality' feature of the LoG. In order to filter the spots by their max intensity, you need to add a spot filter and choose 'Maximal intensity' from the dropdown choice.