TrakEM2-AreaList results

[Alexander Haverkamp]

Dear all,

In a recent project I have labelled cell bodies using TrakEM2 and now I would like to measure the diameter of these.
So far my  approach was, that I would have selected the label of interest in the Project Objects window and select "Measure".
This would than open two new windows of which one is called "AreaList results" . One of the results here is a "max diameter" and I am very tempted to use this value.

However, I would need to have the measurement in µm and I guess that the Area List result is in pixel. Does anyone know how I can convert the result to µm?
If I right-click on the original image stack in TrakEM2 it tells me that the height and the width of a pixel are  0.51 (µm???) and that the depth of the voxel is 0.99 (µm??). Would it now be enough to multiple the "max diameter" with 0.51 or would I also need to consider the voxel depth?

All the best and thank you very much for your help already,

Alexander

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[Albert Cardona-2]

Dear Alexander,

first calibrate your TrakEM2 project:
http://www.ini.uzh.ch/~acardona/trakem2_manual.html#calibration

... then the "maximum diameter" will be in e.g. microns.

If you'd rather do the measurement yourself, obtain the 3d mesh from the
arealist object, iterate its 3d vertices, and compute the diameter with
your own methods. The methods to do so start at AreaList.generateTriangles,
and you can see something similar here:

http://fiji.sc/wiki/index.php/TrakEM2_Scripting#Measure_the_minimal_distance_from_each_ball_to_a_surface_defined_by_a_profile_list

Hope this helps.

Albert




2013/9/22 Alexander Haverkamp <[hidden email]>

> Dear all,
>
> In a recent project I have labelled cell bodies using TrakEM2 and now I
> would like to measure the diameter of these.
> So far my  approach was, that I would have selected the label of interest
> in the Project Objects window and select "Measure".
> This would than open two new windows of which one is called "AreaList
> results" . One of the results here is a "max diameter" and I am very
> tempted to use this value.
>
> However, I would need to have the measurement in µm and I guess that the
> Area List result is in pixel. Does anyone know how I can convert the result
> to µm?
> If I right-click on the original image stack in TrakEM2 it tells me that
> the height and the width of a pixel are  0.51 (µm???) and that the depth of
> the voxel is 0.99 (µm??). Would it now be enough to multiple the "max
> diameter" with 0.51 or would I also need to consider the voxel depth?
>
> All the best and thank you very much for your help already,
>
> Alexander
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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http://albert.rierol.net
http://www.ini.uzh.ch/~acardona/

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