Login  Register

Maximum intensity projection of a set of focal planes in 4d

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
2 messages Options Options
Embed post
Permalink
Reply | Threaded
Open this post in threaded view
| More
Print post
Permalink

Maximum intensity projection of a set of focal planes in 4d

Jeff Hardin
39 posts
Dear ImageJ friends,

We are considering changing our software platform for acquiring  
Yokogawa spinning disc images from Perkin-Elmer Ultraview to Volocity.  
One thing the P-E software is really good at, which also turns out to  
be tough in Volocity, is displaying image stacks from a 4d dataset on  
the fly as projections on the fly. Ultraview allows one to project a  
range of focal planes centered at the currently selected focal plane.  
This doesn't appear to require loading the entire dataset into RAM,  
which is a big plus. We would like to upgrade, since the Ultraview  
software requires Windows 2000. We'd like to move to a more modern  
operating system.

Does anyone know of a way to do this easily in ImageJ? If you know of  
a commercial software platform, I'd appreciate an email off-list.

Thanks in advance,

Jeff
----------------------------------------------
Jeff Hardin
Professor and Chair, Department of Zoology
Director, Biology Core Curriculum
University of Wisconsin
1117 W. Johnson St.
Madison, WI 53706
voice: (608) 262-9634
fax: (608) 262-7319
email: [hidden email]
Reply | Threaded
Open this post in threaded view
| More
Print post
Permalink

Re: Maximum intensity projection of a set of focal planes in 4d

ctrueden
1670 posts
Hi Jeff,

ImageJ should be able to do what you ask, using the macro language. It
should be pretty straightforward to write a macro to do a maximum intensity
projection across a range of image planes, using virtual stacks to avoid
keeping the entire stack in RAM at once.

See the ImageJ website's macro language docs (
http://rsbweb.nih.gov/ij/developer/index.html), particularly "Built-In Macro
Functions" and the "Macros on Website" examples. Assuming there is no
slicker built-in way to do it, you could accomplish your goal by prompting
the user for the center plane index and radius, looping over center-radius
to center+radius, checking pixel values at each (x,y) coordinate, recording
the brightest ones into a new image plane, and finally displaying that image
at the end.

If you want to do it interactively, it is a little more involved, but would
still be pretty easy to accomplish with a plugin.

-Curtis

On Wed, Oct 8, 2008 at 5:07 PM, Jeff Hardin <[hidden email]> wrote:

> Dear ImageJ friends,
>
> We are considering changing our software platform for acquiring Yokogawa
> spinning disc images from Perkin-Elmer Ultraview to Volocity. One thing the
> P-E software is really good at, which also turns out to be tough in
> Volocity, is displaying image stacks from a 4d dataset on the fly as
> projections on the fly. Ultraview allows one to project a range of focal
> planes centered at the currently selected focal plane. This doesn't appear
> to require loading the entire dataset into RAM, which is a big plus. We
> would like to upgrade, since the Ultraview software requires Windows 2000.
> We'd like to move to a more modern operating system.
>
> Does anyone know of a way to do this easily in ImageJ? If you know of a
> commercial software platform, I'd appreciate an email off-list.
>
> Thanks in advance,
>
> Jeff
> ----------------------------------------------
> Jeff Hardin
> Professor and Chair, Department of Zoology
> Director, Biology Core Curriculum
> University of Wisconsin
> 1117 W. Johnson St.
> Madison, WI 53706
> voice: (608) 262-9634
> fax: (608) 262-7319
> email: [hidden email]
>