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

[Jeff Hardin]

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: [phone]
fax: [phone]
email: [hidden email]

[ctrueden]

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: [phone]
> fax: [phone]
> email: [hidden email]
>