How to use "Import from TrackMate..."?

[Putri Aura]

Hi,

I tried to import TrackMate xml track file into TrackManager but failed.

After tracking cells by using TrackMate v3.4.2, the xml file was saved then imported by ICY.

I did the tracking on ICY first or without doing tracking got the same "nothing happened".

Is there something I am supposed to do before importing the xml file? I appreciate any assistance.

Best,

putri

[Stephane]

Hi,

I'm not sure what you're trying to do. The file you joined in your message seems to be tracks coming from the Sequence generator plugin in Icy. I was able to import the tracks correctly in Track Manager even if i got some error messages (Detection object not compatible). do you have the TrackMate file you want to import in Icy ?
Thanks.

- Stephane

[Putri Aura]

Hi Stephane,

There are three drop-down selections on the "File" menu of TrackManager. I used the third "Import from TrackMate..." previously but got nothing on TrackManager.

While I used the first "Load..." menu, the "Celegans-5pc_17timepoints_Icy.xml" could be read. It shows all tracks on TrackManager and on 2D visualization window.

I am sure that TrackManager could lmport xml file from TrackMate by using the "Load..." menu. But I have no idea what the menu "Import from TrackMate..." stands for.

Thank you for your test.

Best,

putri

[Stephane]

Hi Putri,

In fact the "Load..." command just allow you to import tracks previously exported by Track Manager in XML format from the "Save..." command. , if you want to import tracks from TrackMate, you indeed need to use the "Import from TrackMate.." .
The thing is that "Celegans-5pc_17timepoints_Icy.xml" has not be generated by trackmate. It looks like a benchmark tracking made by a Icy plugin.

Best,

- Stephane

[Putri Aura]

Hi Stephane,

I tried to reproduce the results again.

After finished tracking with TrackMate, I used "Export tracks to Icy"  to extract the "Celegans-5pc_17timepoints_Icy.xml".

I made sure again that the "Celegans-5pc_17timepoints_Icy.xml" is able to be imported by using "Load..." rather than "Import from TrackMate...".

The file extracted by TrackMate is saved as XML format so maybe it is read by Icy. However, on the "Console Output" window show many lines of error messages as followed:

********* TrackManager.createDetection('plugins.nchenouard.particleTracking.sequenceGenerator.ProfileSpotTrack', ...) error :

java.lang.NoSuchMethodException: plugins.nchenouard.particleTracking.sequenceGenerator.ProfileSpotTrack.<init>()

The object is maybe not compatible (should have a default constructor with no arguments and extends Detection)

Loading as a the default Detection object.

********* TrackManager.createDetection('plugins.nchenouard.particleTracking.sequenceGenerator.ProfileSpotTrack', ...) error :

java.lang.NoSuchMethodException: plugins.nchenouard.particleTracking.sequenceGenerator.ProfileSpotTrack.<init>()

The object is maybe not compatible (should have a default constructor with no arguments and extends Detection)

Loading as a the default Detection object.

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false

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I will upload the XML format from Fiji and you could try it again.

Thanks again.

Best,

putri

[Stephane]

Hi Putri,

We made some changes to the plugins so now it correctly import the TrackMate export for Icy.
Indeed you have to use the simple "Load.." command as this is an Icy formatted export (to be honest i didn't known TrackMate could do Icy formatted export).
Be sure to do plugin update then after that it should import it correctly :)

Best,

- Stephane

[Putri Aura]

Hi Stephane,

Unfortunately the "Import from TrackMate..."  still is unable to load the XML file extracted from TrackMate. It seems to accept the file but nothing happened. The Celegans-5pc_17timepoints_Icy.xml can only be imported by using "Load..." menu on TrackManager.

I am sure the Spot Tracking plugin did upgrade to v3.4.1.

My system is on Win10 x64. Do you have any suggestion>

Best,

putri

[Stephane]

Can you attach that XML file so i could test and try to understand the problem ?

[Putri Aura]

Hi Stephane, 

Using "Import from TrackMate..." did not see tracks on 2D canvas, the "Tracking groups" shows "no track group available...".

Have a nice weekend.

putri

[Stephane]

Hi Putri,

This file is not intended to be imported with "Import from TrackMate..." command as this is actually Icy formatted tracks. I guess the "Import from TrackMate..." command is for different kind of XML file. Your file should be imported with classic "Load..." and in this case the tracks appears correctly as you already verified :)
What do you expect more than having tracks loaded in Track Manager ?

Best,

- Stephane

[Putri Aura]

Hi Stephane,

Thanks for your confirmation and kindly help.

My colleagues and myself are in the biological background and we do not have experiences in programming skills. Once we need do image processing and analysis, the selection of software become a suffering thing. In my facility we have Imaris, Avizo  and metamorph but none of their maintenance are continued. That is because the high cost of maintenance fee and we only have one license separately. Without maintenance then without supporting makes users like my colleagues and myself want to select alternatives for image analysis. 

We have used imagej and Fiji for quite a long time and we has also noticed that Icy has an excellent 3D VTK display in the early stage. It's a pitty for us that there are so many wonderful plugins and protocols but we don't even know how to adjust those parameters optimally because we did not be trained those "common senses" for used them. It would be helpful if your team could put more tutorial movies. Recently, ImageJ or Fiji face problems with 3D viewer on Java 1.8, so any display mode needs the 3D viewer cannot not work if the Java environment is in v1.8. Thanks to ICY, we could perform the tracking for 2D/3D+t and display the tracks on 3D mode :)

I would like to expect TrackMager has add some functions (maybe it has already possessed) like the subset of  Track's time points (Tail to Head or Head to Tail) instead of displaying the Track in its entirety( the same as "Dragon Tail" function on Imaris spot tracking.

We appreciate your assistance.

Best,

putri

[Stephane]

Hi Putri,

Thanks for taking time to explain your story :) We are well aware that Icy is not well documented and really miss good tutorials.
We are really considering this point and plan to do something about it soon hopefully. We were providing some free trainings here in Pasteur Institute in Paris and sometime outside in some labs when there is at least 10 people interested by the training but because of the lack of time (and also human resource) we are now focusing on providing online tutorials so everyone can access them easily.

In fact what you are asking (sub time selection of tracks) is already available in Icy, you just require to add a specific Track Processor in the Track Manager for that (it's called Time Clipper). You can find here a video example about tracking in Icy here :
https://www.youtube.com/watch?v=APewAXxMkJE

The video is quite old but still show you how to get intensity profile on tracks by adding the "intensity profile" track processor on Track Manager, but you can do much more than that with the different available track processors !

You also have the documentation about Track Manager here :
http://icy.bioimageanalysis.org/plugin/Track_Manager

It's far from being complete and exhaustive but still it explains the basics about how use it.
I hope that will help you :)

Best,

- Stephane

[Putri Aura]

Hi Stephane,

Thank you very much for your assistance.

I look forward to seeing the tutorial movies released online. For this period of time, we keep practicing some functions of Icy.

I will let you know if we need your further help.

Best,

putri