color depth-cueing

[Jan Eglinger-5]

Dear all,

is there an easy way (or a plugin) to color-code z-projections of a stack?

I'm looking for a similar feature like Depth-Cueing in the "3D Project"
dialog, but to assign different colors (instead of intiensities) to the
slices of a (gray) stack before projecting it.

Did anybody do this before?

Thanks,
jan


--
Jan Eglinger
PhD Student, Eckhard Lammert group
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 Dresden
Germany

[Maria Calvo-2]

Dear Jan,
The plugin z code works well for xyz stacks before projection:
http://www.macbiophotonics.ca/imagej/z.htm#z_code

Regards,

Maria Calvo

Jan Eglinger escribió:

> Dear all,
>
> is there an easy way (or a plugin) to color-code z-projections of a stack?
>
> I'm looking for a similar feature like Depth-Cueing in the "3D Project"
> dialog, but to assign different colors (instead of intiensities) to the
> slices of a (gray) stack before projecting it.
>
> Did anybody do this before?
>
> Thanks,
> jan
>
>
>  

... [show rest of quote]

--


___________________________________

Dra. Maria Calvo

Unitat de Microscòpia Confocal
Serveis Cientificotècnics-C.Casanova
Facultat de Medicina
Universitat de Barcelona
C/ Casanova 143
Barcelona 08036

Tel: [phone]/39930
Fax: [phone]
E-mail: [hidden email]
___________________________________

[Wan Ying]

Hi,

I don't see Z-functions/Z Code Stack in menu Plugins/Stacks,i only see Measure Stack. Anywhere i can find/download Z Code Stack?

Thanks,
WY

[Julien Colombelli]

Hi Jan,

If you use Fiji, you find this option implemented in
Image/Hyperstacks/Temporal-Color Code
which works on xyz or xyt stacks too

you get the color projection directly, and can choose the projecting
interval, as well as some LUT choices,
and (last but not least) a color code bar for the depth (or time).

Hope this helps

J


On 23 September 2008 10:19, Jan Eglinger <[hidden email]> wrote:

> Dear all,
>
> is there an easy way (or a plugin) to color-code z-projections of a stack?
>
> I'm looking for a similar feature like Depth-Cueing in the "3D Project"
> dialog, but to assign different colors (instead of intiensities) to the
> slices of a (gray) stack before projecting it.
>
> Did anybody do this before?
>
> Thanks,
> jan
>
>
> --
> Jan Eglinger
> PhD Student, Eckhard Lammert group
> Max Planck Institute of Molecular Cell Biology and Genetics
> Pfotenhauerstrasse 108
> 01307 Dresden
> Germany
>

... [show rest of quote]

--
Julien Colombelli
Advanced Digital Microscopy
Institute for Research in Biomedicine - IRB Barcelona
Baldiri Reixac, 10
Tel:  [phone]
Fax: [phone]
E-08028 Barcelona - Spain
[hidden email]

[Gabriel Landini]

On Thursday 10 Feb 2011 17:46:23 Julien Colombelli wrote:
> If you use Fiji, you find this option implemented in
> Image/Hyperstacks/Temporal-Color Code
> which works on xyz or xyt stacks too

That does not work properly in my Fiji setup (which is up to date) on simple
stacks:
I load the mri-stack sample, run the command
Image/Hyperstacks/Temporal-Color Code

and most of the time I get a "MAX_mri-stack.tif" window which is greyscale.

With the t1-head sample I get a "MAX_colored" image.

I think that there is a loss of track of which image gets processed.

By adding line 81:

80 for (i = 0; i < totalframes; i++) {
81 selectImage(tempID);
82 colorscale = floor((256 / totalframes) * i);

appears to process the mri-stack correctly. Since I do not have any
hyperstacks handy right now, can somebody please test this?
I attached the macro.

Cheers

Gabriel

PS: this is a re-send as the list has rejected the attachment. If you need to
see the complete macro code, see the fiji-devel list.