How to batch process particle tracking ?

[pierre]

Hi There!

 

I really like ICY: Great combination of look, speed and intuitive GUI.

I've been using the Spot Detection / Particle Tracker successfully.

 

Now, I'd like to be able to automate this task to process lots of AVI files.

I've cheked the "protocols" tools but the blocks for spot detection and Particle Tracker are not there yet.

 

Are you planning to add those two plugins in the protocols?

Beside protocols, do you see another way to batch process the AVI file by writing a script or something?

 

thank you!

 

Pierre

[Stephane]

Hi Pierre,

Thanks for your kind comment about Icy :)
There is already a batch processing feature in the Spot detector plugin so it can handle a group of file or a directory but there is nothing like that for the track manager.
Indeed we plan to add block for the spot detector, and now you are talking about, it is important to include the particle tracker too in block form, it can export its result in XML format in a specified directory to start with.

Right now, you can still develop your own Icy plugin in java which just make the batch processing.
If you are interested in that solution, i highly recommend you to use Eclipse with the Icy4Eclipse plugin :
http://www.herve.name/pmwiki.php/Main/Icy4Eclipse

Then have a look on this documentation which provide basics tutorials :
http://icy.bioimageanalysis.org/index.php?display=devDoc

Cheers,

- Stephane

[pierre]

Hi Stephane,

Thank you for your answer.

I indeed noticed the batch processing feature for the Spot Detector which definitely helps.

Using the tutorial links you provided, I will work to develop a batch processing plugins.

Cheers!

Pierre

[Stephane]

Hi Pierre,

Ok, if you need some assistance, free feel to ask there :)

Cheers,

- Stephane