ImageJ Integer LUT / Overlay

[Edward Ando']

Dear ImageJ Community, a bit of a tricky question:

I have a segmented volume of particles, each with a discrete integer
value (first particle value = 1, second particle 2 etc).

I have calculated various data at the particle level (e.g. volume),
which I would like to visualise in my 3D volume. I need what I consider
to be an integer lookup table, so that the label 1 can be looked up to
its volume, label 2 a different volume, etc. This way instead of
labels, I can see the numeric volume as the value for a particular
particle.

I have tried using a calibration but this seems to want to fit curves
to everything.

What is the easiest way to achieve what I want?

Thanks in advance,
Edward Ando

[dscho]

Hi,

On Fri, 20 Aug 2010, Edward Ando' wrote:

> I have a segmented volume of particles, each with a discrete integer
> value (first particle value = 1, second particle 2 etc).
>
> I have calculated various data at the particle level (e.g. volume),
> which I would like to visualise in my 3D volume. I need what I consider
> to be an integer lookup table, so that the label 1 can be looked up to
> its volume, label 2 a different volume, etc. This way instead of labels,
> I can see the numeric volume as the value for a particular particle.

There is the wonderful "Show color surfaces" menu entry in Fiji's
Plugin>Process menu. You can call it after attaching a lookup table (also
known as "color map") to your (8-bit) image.

Beginnings of a documentation are to be found at:

http://pacific.mpi-cbg.de/wiki/index.php/Show_Color_Surfaces

This plugin was written by Mark Longair and uses the 3D Viewer written by
Benjamin Schmid.

So if you find this useful you should cite Mark's and Benjamin's work.

Ciao,
Johannes

[Michael Doube]

Edward,

Check out the particle analyser in BoneJ, which does more or less what
you want, I think.  Anyway, take a look and let me know whether it is
useful (or not).

http://bonej.org/particles

Michael

On 20/08/10 18:11, Edward Ando' wrote:

> Dear ImageJ Community, a bit of a tricky question:
>
> I have a segmented volume of particles, each with a discrete integer
> value (first particle value = 1, second particle 2 etc).
>
> I have calculated various data at the particle level (e.g. volume),
> which I would like to visualise in my 3D volume. I need what I consider
> to be an integer lookup table, so that the label 1 can be looked up to
> its volume, label 2 a different volume, etc. This way instead of
> labels, I can see the numeric volume as the value for a particular
> particle.
>
> I have tried using a calibration but this seems to want to fit curves
> to everything.
>
> What is the easiest way to achieve what I want?
>
> Thanks in advance,
> Edward Ando

[Edward Ando']

Thanks for the replies. The show colour surfaces tool uses the right
kind of data as input, but I need to do a further level of treatment.

In my volume, I have the background = 0 and particles coloured in =
{1,2,3...150,000}.

I have different types of information about these particles, say
density, or volume or temperature, which I know from an external
source, and I would like to visualise this data plotted on the
particles.

I would therefore like to attach an "Integer Lookup Table" to do the
following lookup:

0  -> 0
1  -> temperature of particle 1, say 32.1
2  -> temperature of particle 1, say 24.7
3  -> 56.2
...

and so on so that I see temperature of each grain in my volume. Is
there a way to achieve this with a lookup table, or should I write a
macro that reads in the table above and goes through changing all the
values?

Edward



On Fri, 20 Aug 2010 22:01:48 +0200 (CEST)
Johannes Schindelin <[hidden email]> wrote:

> Hi,
>
> On Fri, 20 Aug 2010, Edward Ando' wrote:
>
> > I have a segmented volume of particles, each with a discrete
> > integer value (first particle value = 1, second particle 2 etc).
> >
> > I have calculated various data at the particle level (e.g. volume),
> > which I would like to visualise in my 3D volume. I need what I
> > consider to be an integer lookup table, so that the label 1 can be
> > looked up to its volume, label 2 a different volume, etc. This way
> > instead of labels, I can see the numeric volume as the value for a
> > particular particle.
>
> There is the wonderful "Show color surfaces" menu entry in Fiji's
> Plugin>Process menu. You can call it after attaching a lookup table
> Plugin>(also
> known as "color map") to your (8-bit) image.
>
> Beginnings of a documentation are to be found at:
>
> http://pacific.mpi-cbg.de/wiki/index.php/Show_Color_Surfaces
>
> This plugin was written by Mark Longair and uses the 3D Viewer
> written by Benjamin Schmid.
>
> So if you find this useful you should cite Mark's and Benjamin's work.
>
> Ciao,
> Johannes
>
>
>
>