Posted by
ctrueden on
Jan 07, 2009; 9:22pm
URL: http://imagej.273.s1.nabble.com/Reslice-stack-at-various-angles-tp3694050p3694051.html
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.zipUnzip 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.html3) 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
>