question

[fallbalah]

Hi,

Your software is great!
I would like to know where can I change the scale?
because i have x40 objectives picture and 0.5µm z-stack and I must put
this data in the software if I want to be exactly?
I didn't find where can i change this?

thank you in advance

[Darren Myatt]

Hi,

The scaling is what most people have queries about in Neuromantic and,
to be honest, it's not implemented in the best way. Basically,
scaling needs to be performed as post-processing after reconstruction,
using Tree Processing->Transformations->Scale Tree from the main
menu. Once the tree has been rescaled it will no longer line up with
the original imagery, but the statistics will be valid (which assume
values in microns, as does the scale bar in the 3D view). As a
result, make sure to save the micron-scaled reconstruction to a
different .swc file, as you don't want to lose the pixel-relative
version.

To do the scaling, you need to work out the microns/pixel of your
images, usually by measuring the pixel size of some known object (from
a reticule or similar). So if something of 1 micron is 40 pixels in
length, then the microns/pixel is 1/40 = 0.025. Put 0.025 as the
scaling factor for X Scaling, Y Scaling and R Scaling (leaving the
offsets as zero, normally, although these allow exact translations to
be added, with the R offset being added for possible shrinkage
compensation). The Z Scaling in your case would be 0.5 (in microns/
slice), although this could be increased appropriately if you know how
much the original sample has decreased in depth since fixing.

I hope this helps,

Darren

[Shirley Beguin]

HI,

thank you very much for your quickly response!!!
Certainly, this is not very fast and easy as method but it works and
that's fine!
it's ok for me!

thank you very much!

--
BEGUIN Shirley
PhD Student
INMED - INSERM U901
Parc Scientifique de Luminy
BP 13
13273 MARSEILLE Cedex 09
Tel.: 04 91 82 81 14

[Darren Myatt]

The scale bar is currently bugged: it dynamically rescales itself according to zoom levels, and there should be text below it showing its current length e.g. 100um.  However, at some point the text rendering got broken, so it isn't hugely useful at the moment.

On Tue, Apr 19, 2011 at 4:49 PM, Shirley Beguin <beg...@inmed.univ-mrs.fr> wrote:

 hi !

I have another question, the scale bar in the 3D view is how many microns??? because i feel that the scale bar in 3D doesn't change when i change the scaling factors?

--
BEGUIN Shirley
PhD Student
INMED - INSERM U901
Parc Scientifique de Luminy
BP 13
13273 MARSEILLE Cedex 09
Tel.: 04 91 82 81 14

--
You received this message because you are subscribed to the Google Groups "NeuromanticUserGroup" group.
To post to this group, send an email to neuromanti...@googlegroups.com.
To unsubscribe from this group, send email to neuromanticuserg...@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/neuromanticusergroup?hl=en-GB.

[Shirley Beguin]