unwinding axons

[Simon Kidd]

Hi,

Iam working with axons where the region of interest is "balled" up (think of a slightly clenched hand). Is there any ImageJ software which would "flatten" the ball? Iam assuming that a open palm is to all intents and purposes topologically the same as the clenched hand, just easier to analyse.

thanks,

Simon

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[Gluender-3]

Dear,

aren't the axons in your images projections of 3D structures onto the
image plane? If so, how do you expect to reveal the lost third
dimension?

However, if the axons are grown on a flat substrate, then you might
search the IJ-archives for lengths measurements or the like.

>Hi,
>
>Iam working with axons where the region of interest is "balled" up
>(think of a slightly clenched hand). Is there any ImageJ software
>which would "flatten" the ball? Iam assuming that a open palm is to
>all intents and purposes topologically the same as the clenched
>hand, just easier to analyse.
>
>thanks,
>
>Simon

Best
--

                   Herbie

          ------------------------
          <http://www.gluender.de>

[Simon Kidd]

Sorry I didnt explain very well, I do actually have the stack the projection came from.

Simon

On 2 Dec, 2009, at 1:19 pm, Gluender wrote:

> Dear,
>
> aren't the axons in your images projections of 3D structures onto the image plane? If so, how do you expect to reveal the lost third dimension?
>
> However, if the axons are grown on a flat substrate, then you might search the IJ-archives for lengths measurements or the like.
>
>> Hi,
>>
>> Iam working with axons where the region of interest is "balled" up (think of a slightly clenched hand). Is there any ImageJ software which would "flatten" the ball? Iam assuming that a open palm is to all intents and purposes topologically the same as the clenched hand, just easier to analyse.
>>
>> thanks,
>>
>> Simon
>
> Best
> --
>
>                  Herbie
>
>         ------------------------
>         <http://www.gluender.de>
>

[Gluender-3]

Well in this case it is a rather involved 3D-task and I'm not aware
if there is a suitable IJ-PlugIn. You may search

        <http://rsb.info.nih.gov/ij/plugins/index.html>


Most promising appear:

-- Mark Longair's "Simple Neurite Tracer" etc.

-- "NeuronJ" (Neurite Tracing and Quantification)

-- "Neuron Morphology "

However, I doubt that 3D unwarping of axons is possible with one of
these packages.

>Sorry I didnt explain very well, I do actually have the stack the
>projection came from.
>
>Simon
>
>On 2 Dec, 2009, at 1:19 pm, Gluender wrote:
>
>>  Dear,
>>
>>  aren't the axons in your images projections of 3D structures onto
>>the image plane? If so, how do you expect to reveal the lost third
>>dimension?
>>
>>  However, if the axons are grown on a flat substrate, then you
>>might search the IJ-archives for lengths measurements or the like.
>>
>>>  Hi,
>>>
>>>  Iam working with axons where the region of interest is "balled"
>>>up (think of a slightly clenched hand). Is there any ImageJ
>>>software which would "flatten" the ball? Iam assuming that a open
>>>palm is to all intents and purposes topologically the same as the
>>>clenched hand, just easier to analyse.
>>>
>>>  thanks,
>>>
>>>  Simon
>>
>  > Best
>  >                  Herbie
>

HTH
--

                   Herbie

          ------------------------
          <http://www.gluender.de>

[Julian Cooper]

Hi Simon,

As you have the stack you may find my radial reslice plugin helpful:

http://rsb.info.nih.gov/ij/plugins/radial-reslice/index.html

I use it to flatten out the acetabulum (hip socket) on a stack of CT images.
This is approximately a hemisphere of bone and can be "flattened" by
applying the radial reslice plugin twice. I imagine from your description
that the same could be done for your axons. To obtain meaningful images the
original stack may have to be rotated appropriately first. The procedure is
a bit involved but is essentially as follows:

1. place a line roi with one end lying on the centre of radial symmetry of
your "ball" and the other end beyond the periphery of the ball
2. use radial reslice to reslice 360° around that end
3. place another line roi on the resulting stack with one end on the centre
of the ball and the other beyond as before
4. use radial reslice again - depending on how "balled" up things are you
may not have to reslice a full 360°. E.g. for the acetabulum 180° is fine as
it is essentially hemispherical.

The resulting stack will be a flattened version of your original stack.

The closer to a sphere the original ball is the better the effect.
Inevitably distortions will be introduced as with any technique to project a
curved surface onto a plane (cf. map projections).

Hope this helps.

Julian

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On
> Behalf Of Simon Kidd
> Sent: 02 December 2009 18:43
> To: [hidden email]
> Subject: Re: unwinding axons
>
>
> Sorry I didnt explain very well, I do actually have the stack
> the projection came from.
>
> Simon
>
> On 2 Dec, 2009, at 1:19 pm, Gluender wrote:
>
> > Dear,
> >
> > aren't the axons in your images projections of 3D
> structures onto the image plane? If so, how do you expect to
> reveal the lost third dimension?
> >
> > However, if the axons are grown on a flat substrate, then
> you might search the IJ-archives for lengths measurements or the like.
> >
> >> Hi,
> >>
> >> Iam working with axons where the region of interest is
> "balled" up (think of a slightly clenched hand). Is there any
> ImageJ software which would "flatten" the ball? Iam assuming
> that a open palm is to all intents and purposes topologically
> the same as the clenched hand, just easier to analyse.
> >>
> >> thanks,
> >>
> >> Simon
> >
> > Best
> > --
> >
> >                  Herbie
> >
> >         ------------------------
> >         <http://www.gluender.de>
> >
>