TrakEM: how to measure apposed surface area

[Luisa de Vivo]

Hi,

I'd like to know whether in TrakEM there is the possibility to measure the
area of two apposed objects and save it as a separate object in the
project, in order to retrieve it in a second moment. I have not found a
clear explanation in the manual.

For instance, I have a stack of images where I'm segmenting a dendritic
spine and its terminal and I want to measure the area  of contact (and its
perimeter) between the two objects. I tried to trace a line between the pre
and post-synaptic objects using the brush tool and saving the segmentation
into an area list, but what I get at the end is not really an area but a
volume, even if I use the brush with minimum size. What do you suggest?

Thank you very much,

Luisa


--
Luisa de Vivo, PhD
Department of Psychiatry
University of Wisconsin
6001 Research Park Boulevard
Madison WI 53719

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Albert Cardona-2]

Dear Luisa,

you could measure the area and divide by two, or use a script to measure the area of the mesh triangles in one side, or use a profile list rather than an arealist.

Best,

Albert

On Aug 22, 2013, at 12:28 AM, Luisa de Vivo <[hidden email]> wrote:

> Hi,
>
> I'd like to know whether in TrakEM there is the possibility to measure the
> area of two apposed objects and save it as a separate object in the
> project, in order to retrieve it in a second moment. I have not found a
> clear explanation in the manual.
>
> For instance, I have a stack of images where I'm segmenting a dendritic
> spine and its terminal and I want to measure the area  of contact (and its
> perimeter) between the two objects. I tried to trace a line between the pre
> and post-synaptic objects using the brush tool and saving the segmentation
> into an area list, but what I get at the end is not really an area but a
> volume, even if I use the brush with minimum size. What do you suggest?
>
> Thank you very much,
>
> Luisa
>
>
> --
> Luisa de Vivo, PhD
> Department of Psychiatry
> University of Wisconsin
> 6001 Research Park Boulevard
> Madison WI 53719
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Luisa de Vivo]

Dear Albert,

thanks for your answer.
I tried to use a profile list and I think it could work for what I need.
However, when I measure the entire profile list folder I get 2 surface
measures. Could you explain in more detail what the interpolated surface is
and how it is computed? Is it more accurate than the sum of length x
thickness? Moreover, how can I measure the perimeter of the area?
Thank you very much for your help.

Luisa


On Thu, Aug 22, 2013 at 5:57 AM, Albert Cardona <[hidden email]> wrote:

> Dear Luisa,
>
> you could measure the area and divide by two, or use a script to measure
> the area of the mesh triangles in one side, or use a profile list rather
> than an arealist.
>
> Best,
>
> Albert
>
> On Aug 22, 2013, at 12:28 AM, Luisa de Vivo <[hidden email]> wrote:
>
> > Hi,
> >
> > I'd like to know whether in TrakEM there is the possibility to measure
> the
> > area of two apposed objects and save it as a separate object in the
> > project, in order to retrieve it in a second moment. I have not found a
> > clear explanation in the manual.
> >
> > For instance, I have a stack of images where I'm segmenting a dendritic
> > spine and its terminal and I want to measure the area  of contact (and
> its
> > perimeter) between the two objects. I tried to trace a line between the
> pre
> > and post-synaptic objects using the brush tool and saving the
> segmentation
> > into an area list, but what I get at the end is not really an area but a
> > volume, even if I use the brush with minimum size. What do you suggest?
> >
> > Thank you very much,
> >
> > Luisa
> >
> >
> > --
> > Luisa de Vivo, PhD
> > Department of Psychiatry
> > University of Wisconsin
> > 6001 Research Park Boulevard
> > Madison WI 53719
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Luisa de Vivo, PhD
Department of Psychiatry
University of Wisconsin
6001 Research Park Boulevard
Madison WI 53719

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Albert Cardona-2]

Dear Luisa,

I refer you to the source code of TrakEM2. Look up the AreaList and
Area*java files, and the Display3D.java, for most details on what you want:

http://repo.or.cz/w/trakem2.git

Albert


2013/8/22 Luisa de Vivo <[hidden email]>

> Dear Albert,
>
> thanks for your answer.
> I tried to use a profile list and I think it could work for what I need.
> However, when I measure the entire profile list folder I get 2 surface
> measures. Could you explain in more detail what the interpolated surface is
> and how it is computed? Is it more accurate than the sum of length x
> thickness? Moreover, how can I measure the perimeter of the area?
> Thank you very much for your help.
>
> Luisa
>
>
> On Thu, Aug 22, 2013 at 5:57 AM, Albert Cardona <[hidden email]>
> wrote:
>
> > Dear Luisa,
> >
> > you could measure the area and divide by two, or use a script to measure
> > the area of the mesh triangles in one side, or use a profile list rather
> > than an arealist.
> >
> > Best,
> >
> > Albert
> >
> > On Aug 22, 2013, at 12:28 AM, Luisa de Vivo <[hidden email]> wrote:
> >
> > > Hi,
> > >
> > > I'd like to know whether in TrakEM there is the possibility to measure
> > the
> > > area of two apposed objects and save it as a separate object in the
> > > project, in order to retrieve it in a second moment. I have not found a
> > > clear explanation in the manual.
> > >
> > > For instance, I have a stack of images where I'm segmenting a dendritic
> > > spine and its terminal and I want to measure the area  of contact (and
> > its
> > > perimeter) between the two objects. I tried to trace a line between the
> > pre
> > > and post-synaptic objects using the brush tool and saving the
> > segmentation
> > > into an area list, but what I get at the end is not really an area but
> a
> > > volume, even if I use the brush with minimum size. What do you suggest?
> > >
> > > Thank you very much,
> > >
> > > Luisa
> > >
> > >
> > > --
> > > Luisa de Vivo, PhD
> > > Department of Psychiatry
> > > University of Wisconsin
> > > 6001 Research Park Boulevard
> > > Madison WI 53719
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
>
>
> --
> Luisa de Vivo, PhD
> Department of Psychiatry
> University of Wisconsin
> 6001 Research Park Boulevard
> Madison WI 53719
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

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