Topography and TopoJ plugin

[Graham Wright]

Hi,

Can anyone direct me where to where I can get the TopoJ plugin (there
are emails in the archives from 2008/2009 from David Hovis saying he
wrote it)?

In case there is something else similar/alternative out there:
I have several z-stacks acquired on a confocal in reflection mode.
They are dental molds on a small scale. Some have teeth and are
therefore rough, others are toothless and therefore smooth. Two things
I want to be able to do:
1) have some means of quantifying rough versus smooth, and
2) create topological images/heat maps.

Thanks,
Graham

Graham Wright, PhD
Temasek Life Sciences Laboratory (TLL)
Singapore

[GCH-2]

I wrote a simple plugin for sometime ago for creating topography  
images from a confocal stack (http://www.gcsca.net/IJ/ 
SurfTool_1b.java). Compile and enter the slice spacing. This was  
never completely finished, but may help.
The roughness of the created topography images can then be estimated  
with the SurfCharJ plugin: http://www.gcsca.net/IJ/SurfCharJ.html

Let me know if this helps.

Gary.

On Aug 13, 2010, at 10:40 AM, Graham Wright wrote:

> Hi,
>
> Can anyone direct me where to where I can get the TopoJ plugin (there
> are emails in the archives from 2008/2009 from David Hovis saying he
> wrote it)?
>
> In case there is something else similar/alternative out there:
> I have several z-stacks acquired on a confocal in reflection mode.
> They are dental molds on a small scale. Some have teeth and are
> therefore rough, others are toothless and therefore smooth. Two things
> I want to be able to do:
> 1) have some means of quantifying rough versus smooth, and
> 2) create topological images/heat maps.
>
> Thanks,
> Graham
>
> Graham Wright, PhD
> Temasek Life Sciences Laboratory (TLL)
> Singapore

[David Hovis]

Graham,

I sent you the TopoJ package off the list.   If anyone else needs it, just email me and I'll send it.

Getting it up and listed for ImageJ and/or included in FIJI has been on my To Do list for a while.

--David




On Aug 13, 2010, at 4:40 AM, Graham Wright wrote:

> Hi,
>
> Can anyone direct me where to where I can get the TopoJ plugin (there
> are emails in the archives from 2008/2009 from David Hovis saying he
> wrote it)?
>
> In case there is something else similar/alternative out there:
> I have several z-stacks acquired on a confocal in reflection mode.
> They are dental molds on a small scale. Some have teeth and are
> therefore rough, others are toothless and therefore smooth. Two things
> I want to be able to do:
> 1) have some means of quantifying rough versus smooth, and
> 2) create topological images/heat maps.
>
> Thanks,
> Graham
>
> Graham Wright, PhD
> Temasek Life Sciences Laboratory (TLL)
> Singapore

[Wan Ying]

Dear David,

Can you please send me the TopoJ Package?

Thanks,
Wan Ying

[dscho]

Hi,

On Fri, 4 Feb 2011, Wan Ying wrote:

> Can you please send me the TopoJ Package?

It is included in Fiji: http://pacific.mpi-cbg.de/TopoJ (you will also
find a link to the sources if you need to understand how it is working
exactly).

Ciao,
Johannes

[David Hovis]

TopoJ is now included with the FIJI distribution of ImageJ.  It is found under the Analyze menu.

Sent from my iPhone
(in case you were wondering why this message was short and full of typos)

On Feb 4, 2011, at 7:50 AM, Wan Ying <[hidden email]> wrote:

> Dear David,
>
> Can you please send me the TopoJ Package?
>
> Thanks,
> Wan Ying
> --
> View this message in context: http://imagej.588099.n2.nabble.com/Topography-and-TopoJ-plugin-tp5419267p5992443.html
> Sent from the ImageJ mailing list archive at Nabble.com.

[Wan Ying]

Thanks Johaness and David. But I did not see any TopoJ under Analyze in FIJI. i downloaded FIJI on nov 2010. do i have to download FIJI again or there's TopoJ plugin available?

Thanks.

[dscho]

Hi,

On Sun, 6 Feb 2011, Wan Ying wrote:

> [...] Johaness [...]

... close :-)

> [...] I did not see any TopoJ under Analyze in FIJI.

It has been released August 18th, 2010. When you start Help>Update Fiji,
type "topo" in the search box on the top and select "View all plugins"
from the combobox below the search box, you should see it. It may be not
installed, for any of a number of reasons.

Note that the updater does not have a chance if your Fiji.app directory is
not writable. This is the case if you are running Fiji from a .dmg that
you downloaded, but where you never dragged the Fiji icon into the
Applications folder.

Ciao,
Johannes

[Wan Ying]

All right, thanks for your suggestion Johannes *sorry for the typo*.
I will check on whether thats the cause.

Thank you! :-)

On Sun, Feb 6, 2011 at 10:31 PM, Johannes Schindelin <
[hidden email]> wrote:

> Hi,
>
> On Sun, 6 Feb 2011, Wan Ying wrote:
>
> > [...] Johaness [...]
>
> ... close :-)
>
> > [...] I did not see any TopoJ under Analyze in FIJI.
>
> It has been released August 18th, 2010. When you start Help>Update Fiji,
> type "topo" in the search box on the top and select "View all plugins"
> from the combobox below the search box, you should see it. It may be not
> installed, for any of a number of reasons.
>
> Note that the updater does not have a chance if your Fiji.app directory is
> not writable. This is the case if you are running Fiji from a .dmg that
> you downloaded, but where you never dragged the Fiji icon into the
> Applications folder.
>
> Ciao,
> Johannes
>
>

[dscho]

Hi,

On Sun, 6 Feb 2011, wan ying choo wrote:

> All right, thanks for your suggestion Johannes *sorry for the typo*.

Hey, no problem! I mistype it sometimes myself :-)

> I will check on whether thats the cause.

I'd be interested in the progress.

Ciao,
Johannes

[Wan Ying]

Hi,

I've got TopoJ installed via FIJI updater. Thanks alot for your help Johannes.

Wan Ying

On Sun, Feb 6, 2011 at 11:03 PM, Johannes Schindelin [via ImageJ] <[hidden email]> wrote:

Hi,

On Sun, 6 Feb 2011, wan ying choo wrote:

> All right, thanks for your suggestion Johannes *sorry for the typo*.

Hey, no problem! I mistype it sometimes myself :-)

> I will check on whether thats the cause.

I'd be interested in the progress.

Ciao,
Johannes

---

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