Track manager in protocols/batch

[Veijo]

Hi!

I love using icy for spot detector and particle tracking, I think the particle tracking works really well and is intuitive to adjust the parameters.
However, to speed up my workflow, I was wondering if there was any way to batch process timelapse sequences to do spot detection, particle tracking and export results (such as instant speed or msd) in bact format. In the protocols module I cannot find the track manager option. I saw some talk about this on this forum previously, but these posts were quite old, so I am wondering wether any updates on this matter have been done or are in planning.

So basically I'd like to open sequnce, do spot detection and particle tracking (always with same settings as they work great) and export for example the instant speed files to csv or similar, but do this in batch mode.

Thanks for a great software!

Kindly,
Veijo

[Stephane]

Hi Veijo,

Sorry for the late reply ! In fact you can already do a bit of tracking quantification with Protocols.
You can type "Spot tracking" in the search bar and you should find the "Spot tracking with excel export" protocol i the result list.
Just open it, it will download required plugins if you don't have it.
This protocols show you a basic example about doing tracking from protocol but currently you only have basic tracks export (Track XLS Export block). We will try to add the "Motion Profiler" processor (which provide many useful information) soon in protocols format. In the meantime, maybe you can try to use some javascript inside your protocol to get the MSD information out of the track data (using existing processor or your own code).

Best,

- Stephane

[Stephane]

For what it worths we just published a new protocol: Spot Tracking with tracks filtering and motion excel export
It shows how to do more advanced tracking operations through protocol.
We just updated the Motion Profiler plugin to allow that.

Best,

- Stephane

Le jeudi 5 avril 2018 20:40:24 UTC+2, Veijo a écrit :

[Veijo]

Hi!

Thank you very much! This is most useful! Excellent!

I'd have one tiny suggestion for the "spot tracking set parameters" block. Now some of the names for the fields (and the order of the parameters) are little bit different than in the actual spot tracking interface. While I think I figured out which correspond to which, it might be even easier to use if they would be named same between the two. For example, the termination threshold and MHT depth are not instantly obvious in terms of the spot tracking interface.

kindly,

Veijo

[Stephane]

Hi Veijo,

Thanks for your feedback and remarks :) In fact even if i wrote the "Block" version of the plugin, i'm not the original author of Spot Tracking and so i simply re-used the name of the internal fields that original programmer used. I just updated the plugin to change parameters names and order a bit in 'Expand Parameters' and 'Set Parameters' blocks, hope that help ;)

Best,

- Stephane