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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 |
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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: 34 934037159/39930 Fax: 34 934039946 E-mail: [hidden email] ___________________________________ |
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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 |
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In reply to this post by Jan Eglinger-5
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: +349340-20451 Fax: +34934031116 E-08028 Barcelona - Spain [hidden email] |
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In reply to this post by Jan Eglinger-5
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. |
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