3D Deformation Profiler on Track Manager

[Bonora Massimo]

Dear Icy Team,

I am new on Icy and I get here looking for good tools for tracking 3D particles in time. I found the tracking options on Icy extremely interesting, but I get an issue that I can't solve, so I am looking for help.

The problem is as follow:

- I obtain objects by thresholding with the HK-mean ("Export ROIs" and "Prepare for tracking" selected).

- Using the Spot Tracking plugin I obtain tracks of the particles.

- I open the track manager plugin to obtain information about volume and shape of each particle along the track using the 3D Deformation Profiler processor, but I can't get any data. Even if the tracks are well represented in my original Image the 3D Deformation Profiler return a tabe with correct amount of time points, correct number of tracks, but no numbers at all.

I feel like I am missing a fundamental step in the process, but I can't understand with one.

Could you provide any suggestions?

Thank in advance!

Massimo

[Alexandre Dufour]

Hi Massimo,

Unfortunately the “3D Deformation Profiler” only works on ROIs built using the “Active Contours” plug-in (exported as “Polygon”). This is why you are seeing an empty table.

I am in the process of updating this tool to fix this limitation, and hopefully can release this in the coming days/weeks.

Cheers

Alexandre

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[Bonora Massimo]

Dear Alexandre,

thanks for suggestions, ROIs built with the “Active Contours” plug-in actually correct the issue.

I actually found that the Active contours require large amount of resources and time from my laptop compared to the HK-mean.

Could yo provide any suggestions about how to reduce the time for execution?

Thank you in advance

Massimo

[Alexandre Dufour]

Hi Massimo,

Typically you can increase execution time by playing with the “contour sampling”, “evolution time step” and “convergence criterion” parameters (NB: some of these options only appear if you check the “advanced options” check box at the top). Increasing speed also comes at a cost though: the cleaner the data (signal/noise ratio), the faster you can run it, but if you do have some noise in the data, then the efficiency might not be as high as expected.

Cheers

Alexandre

To view this discussion on the web visit https://groups.google.com/d/msgid/icy-software/bd02c33c-7e9b-4f0f-a4aa-5db1288b89ed%40googlegroups.com.