Track processor gate ROI : How to select the tracks

[Eric]

Hi all,
I want the statistics from the "track processor speed statistics" only from the tracks presented by the "Track processor gate".
In the image the "Track processor gate" is drawing  the tracks I want, but I don't understand how to select them or delete the others.
Any suggestion ?

Thanks

[Alexandre Dufour]

Hi Eric,

I’m currently rewriting the speed statistics filter to improve the output and handle the selection of tracks you mentioned.

As I do this, I realise that the statistics that I calculate are a bit heterogeneous: some refer to displacements (absolute/relative), some refer to speed (min/max/avg), while obviously speed can be recovered from displacement. Would it make sense if the entire table is expressed in displacement rather than speed? Or should I leave it as it is now? Or should I present both (although they are redundant)?

(And I am writing the documentation alongside, as you requested quite some time ago already!)

Let me know your thoughts on this

Cheers,

Alexandre

---

Alexandre Dufour, Ph.D.

Institut Pasteur - Bio Image Analysis Group

25, rue du Docteur Roux, Paris, France

Research: http://www.bioimageanalysis.org/dufour

Software: http://icy.bioimageanalysis.org

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[Alexandre Dufour]

Hi again,

So since I didn’t have any news, I went on to “guess" what you would like and published a major update of the plug-in, which I also renamed to Motion Profiler (don’t worry, it will still update automatically). Basically I rewrote it entirely (I needed to for my own projects anyway), will the following improvements:

 — Display displacement or speed, in pixel or real units

 — All statistics can be exported to .xls

 — Plot displacement profiles in 2D and 3D (replaced JFreeChart by another library that allows raw data export)

 — Statistics are aware of the “filtered” tracks (so your ROI gate will now work with it).

 — And I wrote a small documentation online!

Have a go at it and let me know if that suits you (and perhaps update your rating ;))

Cheers,

Alexandre

To view this discussion on the web visit https://groups.google.com/d/msgid/icy-software/2D7BE533-E2EE-49CB-9A4D-32C0DD80F24E%40pasteur.fr.

[Eric]

Hi Alexandre,
So cool that you are working on it !!!! Here are our suggestions :
We are interested in speed parameters, so for us datas are ok like they are. Moreover, the min and max speed won't be available if only displacement are presented (except if you give all the displacements for every track at every t ).

The only 3 (4 in fact )  things we are interested are : Get the speed statistics for tracks 
1) of a specific length (can be done in excel anyway)
2) Tracks that cross a specific ROI
3) Both Length and through ROI

4) Direct export of the file (can be done by copy past if you work on few files).

That's all for today !!!!
Thanks a lot !!!!

[Alexandre Dufour]

Hi Eric,

I guess many of the questions you asked will now be answered by the update I published. Let me know when you’ve tried it and see if that is enough.

Alexandre

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[Eric]

Hi Alexandre,
I just tried your "Motion Profiler". I gated the Tracks with ROI and Length : it is perfect !!!!
I  displayed Real Units : Seems OK.
We will be using the Tracking plugin next week so we will have a better experience but I immediately give 4 stars !!!!! (leave me 2 minutes though !)
Merci and Muchas Gracias from Lety and Rodrigo who will be using it too !!!!

Le mardi 17 juin 2014 18:52:39 UTC+2, Eric a écrit :

[Alexandre Dufour]

Hi again Eric,

Thanks for your feedback… But I didn’t stop there. I actually realised that I could easily filter the tracks based on the computed statistics, so I’ve just published another update where you can switch from the default “statistics” view to a “filter” view, where you can select filtering criterion and value. This filtering also affects the following track processors as you might expect, so you may absolutely combine multiple instances of the motion profiler to filter precisely the tracks you want before (or after) computing statistics on them.

Hope you’ll enjoy this as well (and I’m sure you won’t be alone…)

Alexandre

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[Eric]

You are too fast.
I am just out of breath !!!
I better watch the football game !!!

Aller les bleus !!!

Le mardi 17 juin 2014 18:52:39 UTC+2, Eric a écrit :