Reslice stack at various angles

[Bob Nienhuis]

Is there a way to do a reslice of an image stack at some
arbitrary angle in the Z axis?

I understand that reslice allows you to draw a line
in the XY plane of a stack and create a new
slice orthogonal to that plane.

I want to reslice in various angles in the Z axis.

I realize this can be computationally  intensive,
but I will be doing this on small cropped stacks
on a 64 bit quad core system.

Bob Nienhuis
UCLA / VA Medical Center

[J. Anthony Parker]

You might look at Reorient3_TP, http://www.med.harvard.edu/JPNM/ij/plugins/Reorient3TP.html 
.  It may be more general than you are looking for, but I think it  
will do what you want.  It is part of an "Align Stacks" package, http://www.med.harvard.edu/JPNM/ij/plugins/ 
.  The Alignment plugin has a manual which explains how it works.  
Several of the operations are the same or similar.

Tony
J. Anthony Parker, MD PhD
[hidden email]
tel [phone] fax -2185 comp -5275
page 617 632-7243 #31978
330 Brookline Ave, Boston, MA, 02215-5400


On Jan 7, 2009, at 2:56 PM, Bob Nienhuis wrote:

> Is there a way to do a reslice of an image stack at some
> arbitrary angle in the Z axis?
>
> I understand that reslice allows you to draw a line
> in the XY plane of a stack and create a new
> slice orthogonal to that plane.
>
> I want to reslice in various angles in the Z axis.
>
> I realize this can be computationally  intensive,
> but I will be doing this on small cropped stacks
> on a 64 bit quad core system.
>
> Bob Nienhuis
> UCLA / VA Medical Center
>

[ctrueden]

Hi Bob,

I wrote a program called VisBio that can do this. To help you out, I have
adapted it into an ImageJ plugin that you can use for arbitrary slicing. You
can download the plugin here:

http://www.loci.wisc.edu/software/visbio-arbitrary-slicer.zip

Unzip the archive into your ImageJ plugins folder. Next time you run ImageJ,
there will be a new VisBio submenu with an "Arbitrary Slicer" item.

This plugin comes with a number of caveats:

1) The bundle is quite large (>5MB zipped, >10MB uncompressed).

2) Like several other 3D plugins for ImageJ, this plugin requires Java3D. If
you have Mac OS X, you're already got it. If you have Windows or Linux, you
can download and install Java3D from:
https://java3d.dev.java.net/binary-builds.html

3) I hacked this together really quickly based on my latest VisBio source,
and it is not well integrated with ImageJ. You need to specify a file on
disk to load, and it may not work with every file format. It should work
with most of the ones supported by Bio-Formats, though.

4) It will take an obnoxiously long time to load. Expect to wait >60 seconds
for VisBio to start up, do some preloading, read your dataset, construct the
slice, construct the display, and load the data into the display. However,
once it's ready, it should be pretty snappy on a reasonably modern machine.

5) You can take a screenshot of the slice either using the Capture tab, or
just using your OS'es screen capture facility.

I have been planning to integrate VisBio into ImageJ better at some point,
but have not had time or funding to do so. Eventually I hope to refactor
VisBio from a big honkin' standalone program into a suite of ImageJ plugins,
though. :-)

Since this plugin is essentially a bundle of VisBio in its entirety, there
is a lot of power:

* In the arbitrary slice controls, first select your yaw, pitch and
location. You should get a realtime (but blocky) view of your slice when
moving these around. When ready, crank the Resolution slider up to max to
get the best quality slice. If you want to move the slice around again after
that, though, either turn down the resolution again or uncheck the
"recompute slice on the fly" checkbox.

* You can overlay the original image stack by clicking the "Data" tab in the
display controls, selecting your dataset filename in the list, then using
"Visible" checkbox and "Toggle slices" button to control which slices are
shown.

* You can control the colors by selecting your dataset and clicking the
"Colors" button.

* Rotate the display by dragging with the right mouse button. Zoom by
holding Shift, and pan by holding Control.

* You can navigate between timepoints and channels in your dataset (if any)
using the sliders on the bottom right of the display.

* There are tons of other features, which you can read about using VisBio's
built in manual accessible from the Help menu.

Hope that helps, and let me know if you have any questions!

-Curtis

On Wed, Jan 7, 2009 at 1:56 PM, Bob Nienhuis <[hidden email]> wrote:

> Is there a way to do a reslice of an image stack at some
> arbitrary angle in the Z axis?
>
> I understand that reslice allows you to draw a line
> in the XY plane of a stack and create a new
> slice orthogonal to that plane.
>
> I want to reslice in various angles in the Z axis.
>
> I realize this can be computationally  intensive,
> but I will be doing this on small cropped stacks
> on a 64 bit quad core system.
>
> Bob Nienhuis
> UCLA / VA Medical Center
>

[Glen MacDonald]

Dear Bob,
That is under Image/Stacks/Reslice
Select a line tool, draw your line ROI, then invoke the command.  Also  
the hotkey is "/".  You are not limited to a straightline selection.  
Creating a rectangular box ROI allows reslicing from top, bottom,  
left, right to create an orthogonal stack.
There is a plugin for cutting planes, but don't have the name at  
hand.  Do a search in the listserv archives.

Regards,
Glen

On Jan 7, 2009, at 9:00 PM, IMAGEJ automatic digest system wrote:

> From: Bob Nienhuis <[hidden email]>
> Date: January 7, 2009 11:56:01 AM PST
> Subject: Reslice stack at various angles
>
>
> Is there a way to do a reslice of an image stack at some
> arbitrary angle in the Z axis?
>
> I understand that reslice allows you to draw a line
> in the XY plane of a stack and create a new
> slice orthogonal to that plane.
>
> I want to reslice in various angles in the Z axis.
>
> I realize this can be computationally  intensive,
> but I will be doing this on small cropped stacks
> on a 64 bit quad core system.
>
> Bob Nienhuis
> UCLA / VA Medical Center

[Aryeh Weiss]

We are having a problem with using global variables in macros. A var declaration
at the beginning of the macro file seems to cause everything to hang.

For example, here is a small macro copied from a previous posting on the subject:

//================

var x;

macro "test" {
    x=10;
    f();
    print (x);
    exit("Terminating normally...");
}

function f(){
      x = 20;
}

//=================

If I omit var x; declaration, then it runs fine (but of course it prints
that x is 10, as expected).

If I include the var x; declaration, then it hangs. I ran it with the debugger
and single step. It advances past the var declaration and highlights the
macro "test" { line. There it stops (ie, cntl-E will not advance operation to
the next line).

It seems something obvious that I missed. I did not find this problem in the
archives.

--aryeh
--
Aryeh Weiss
School of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

[Michael Schmid]

Hi Aryeh,

as far as I understand it, global variables work with installed  
macros only, not if you use "run macro" form a text window. Your test  
macro works well if you install it.

Use Macros>Install Macros in the text window's menu or ctrl-i (Mac:  
cmd-i)

Michael
________________________________________________________________

On 14 Jan 2009, at 11:58, Aryeh Weiss wrote:

> We are having a problem with using global variables in macros. A  
> var declaration at the beginning of the macro file seems to cause  
> everything to hang.
>
> For example, here is a small macro copied from a previous posting  
> on the subject:
>
> //================
>
> var x;
>
> macro "test" {
>    x=10;
>    f();
>    print (x);
>    exit("Terminating normally...");
> }
>
> function f(){
>      x = 20;
> }
>
> //=================
>
> If I omit var x; declaration, then it runs fine (but of course it  
> prints
> that x is 10, as expected).
>
> If I include the var x; declaration, then it hangs. I ran it with  
> the debugger and single step. It advances past the var declaration  
> and highlights the
> macro "test" { line. There it stops (ie, cntl-E will not advance  
> operation to the next line).
>
> It seems something obvious that I missed. I did not find this  
> problem in the archives.
>
> --aryeh
> --
> Aryeh Weiss
> School of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: [phone]
>

[Wayne Rasband]

This bug is fixed in the ImageJ 1.42h daily build. Pressing ctrl-r
(Macros>Run Macro) in the macro editor now runs the first macro in a
macro set regardless of whether or not there are global variables. This
means you can now also debug the first macro in a macro set by pressing
ctrl-d (Debug>Debug Macro) and single step through the code by pressing
ctrl-e (Debug>Step). On the Mac you can debug any macro in a macro set
by running it from the Macros menu with the alt key down. This does not
work on Windows because of a Java bug.

-wayne


On Jan 15, 2009, at 3:05 PM, Wayne Rasband wrote:

> We are having a problem with using global variables in macros. A var
> declaration
> at the beginning of the macro file seems to cause everything to hang.
>
> For example, here is a small macro copied from a previous posting on
> the subject:
>
> //================
>
> var x;
>
> macro "test" {
>     x=10;
>     f();
>     print (x);
>     exit("Terminating normally...");
> }
>
> function f(){
>       x = 20;
> }
>
> //=================
>
> If I omit var x; declaration, then it runs fine (but of course it
> prints
> that x is 10, as expected).
>
> If I include the var x; declaration, then it hangs. I ran it with the
> debugger
> and single step. It advances past the var declaration and highlights
> the
> macro "test" { line. There it stops (ie, cntl-E will not advance
> operation to
> the next line).
>
> It seems something obvious that I missed. I did not find this problem
> in the
> archives.
>
> --aryeh
> --
> Aryeh Weiss
> School of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: [phone]
>