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

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

Dear Confocal 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]


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

Jeff Hardin wrote:

> Dear Confocal 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.
I cannot tell if there is a plugin, but writing a *simple* one isn't
that much work. getting it to work with a broad range of formats and
interact with other tools properly, would be work.
depending on how quick you need it, this feature is supported in the
next major version of endrov (3.x, www.endrov.net), runs on all
operating systems.

/Johan

>
> 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]
>
>


--
--
------------------------------------------------
Johan Henriksson
MSc Engineering
PhD student, Karolinska Institutet
http://mahogny.areta.org http://www.endrov.net
Jason Swedlow Jason Swedlow
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Re: Maximum intensity projection of a set of focal planes in 4d

Hi All-

The OME Consortium has been working on a MIP facility within OMERO for the last few months. We've just released this as OMERO-Beta3.1 (see our OMERO Downloads page at http://openmicroscopy.org/site/downloads/omero-downloads for more info).  OMERO applications run on all major operating systems and of course are open source and freely available.

For info on running and installing, see our video screencast pages at

http://openmicroscopy.org/site/videos

and installation instructions at

http://trac.openmicroscopy.org.uk/omero/wiki/OmeroInstall

Cheers,

Jason


On Thu, Oct 9, 2008 at 7:47 AM, Johan Henriksson <[hidden email]> wrote:
Jeff Hardin wrote:
> Dear Confocal 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.
I cannot tell if there is a plugin, but writing a *simple* one isn't
that much work. getting it to work with a broad range of formats and
interact with other tools properly, would be work.
depending on how quick you need it, this feature is supported in the
next major version of endrov (3.x, www.endrov.net), runs on all
operating systems.

/Johan

>
> 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]
>
>


--
--
------------------------------------------------
Johan Henriksson
MSc Engineering
PhD student, Karolinska Institutet
http://mahogny.areta.org http://www.endrov.net



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Wellcome Trust Centre for Gene Regulation & Expression
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