Spot Tracking finally compatible with Script and Protocols !

[Stephane]

Hi folks,

Good news : we finally modified the Spot Tracking plugin to make it compatible with Script and Protocols. We know that a lot of people wanted to do tracking in batch processing, that is now finally possible in Icy :) Note that only the new MHT Tracker is available (legacy tracker is not yet compatible).

Here are the methods available for Script :

// Get estimated tracking parameters from a set of detection
SpotTracking.estimateParameters(..)        
// Get tracking parameters from a file
SpotTracking.loadParameters(..)
// Save tracking parameters into a file
SpotTracking.saveParameters(..)
// Process tracking from a set of detection and get result tracks
SpotTracking.executeTracking(..)

And for Protocol, you have now access to the following blocks :

// Get estimated tracking parameters from a set of detection
Spot Tracking Estimate Parameters
// Get tracking parameters from a file
Spot Tracking Load Parameters
// Expand tracking parameters structure into several variables (for manual modification)
Spot Tracking Set Parameters
// Set / modify tracking parameters manually
Spot Tracking Set Parameters
// Save tracking parameters into a file
Spot Tracking Save Parameters
// Process tracking from a set of detection and get result tracks
Spot Tracking Do Tracking

Not that you need to install the new "Spot Tracking Blocks" plugin to get access to these new blocks, they are not directly included inside the Spot Tracking plugin.

All these changes allow you to retrieve "tracks data" from Script and Protocol but to extracts information from these tracks you need TrackManager. Currently only the "XLS Tracks export" processor has been modified to support Script and Protocol so you can at least have all your tracks in an excel table to work with... but soon we plan to update some others Track Processor as "Motion Profiler" to take advantage of Script and Protocol.

Best,

- Stephane

[Stephane]

You can find an example protocol to use Spot tracking here :
http://icy.bioimageanalysis.org/protocol/Spot_Tracking_with_excel_export

[Putri Aura]

Hi Stephane,

Many of my colleagues include myself would like to use Icy because its 3D VTK for rendering visualization is excellent.

We use spot tracking plugin for a while and want to know whether the tracks could be linked to 3D VTK, for example,

trajectory of each track could also display on 3D VTK. For now those trajectories are only on default 2D canvas. It will be exciting If it could do.

Best,

putri

[Alexandre Dufour]

Hi Putri,

To get the tracks visible in VTK, you can install the "Track Painter" plugin. This plugin is an alternative to the default painter, and works for both the 2D and 3D views.

Once installed, you will be able to add it from the list of track processors within the track manager

NB: this plugin should be installed *before* performing the actual detection+tracking steps, otherwise the track manager won't see the new plugin. 

Alexandre

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[Putri Aura]

Hi Alexandre,

Thank you for the direction.

The 3D VTK can display tracks by using "Track Painter" plugin now.

Best,

putri

[kobi]

Hi Stephane,

I used a lot the detection and tracking tools in Icy last year. It was working well. I wanted reuse it now and for a reason I did not understand, the spot detection tool is not working at all! I tested it on a same image as last year and I got no detection! I am disappointed because I have no idea what is wrong! The fact that you did recent modifications, could be that a reason of my problems?

Thanks in advance of your help.

Best Regards,

Dominique.

[kobi]

Finally, I fixed the problem...

Sorry for spaming!

Dom

[Stephane]

I guess the problem comes fro the fact that default parameters changed ;)

[David G]

Hi Stephane,

Thanks very much, it is a really useful functionality and  protocol! :)

Do you know how I can get the tracks information from the exported XLS file back into Track Manager please?

Many thanks for your help,

David

[Stephane]

Hi David,

You cannot import tracks from the XLS output, currently the Track Manager itself does not directly interact with Protocols.
What do you intent to do exactly ? We can probably find some solutions as having new blocks to do the tracks XML import/export from/to the Track Manager.

Best,

- Stephane