Re: Is a Microscopy application possible?

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Re: Is a Microscopy application possible?

pieper
Administrator
Hi Holger -

In general is not optimized for the tasks you describe, but some
experimentation has been done in this area.  See for example these notes:

http://massmail.spl.harvard.edu/public-archives/slicer-users/2010/002589.html

If you need a large-memory build, we suggest using the linux-x86_64
builds and a machine with lots of memory.  Or down-sample the data using
a tool like imagemagick or IrfanView on windows.  Also note that while
slicer will load and display RGB images, many modules only work with
grayscale data.

HTH,
Steve

On 01/12/2011 05:23 AM, Holger Lange wrote:

> not sure what went wrong ... I subscribed
>
> On Wed, Jan 12, 2011 at 10:47 AM, <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     To control spam, only subscribers can post to this list.  Please
>     subscribe and resend.
>
>
>
>     ---------- Forwarded message ----------
>     From: Holger Lange <[hidden email]
>     <mailto:[hidden email]>>
>     To: [hidden email] <mailto:[hidden email]>
>     Date: Wed, 12 Jan 2011 10:47:43 +0100
>     Subject: Is a Microscopy application possible?
>     Dear Slicer Users,
>
>     I am looking for the right 3D visualization tool for a 3D stack of
>     microscopy slides. I got plain 24bit color TIF or JPEG files to
>     start with.
>
>     1) Is there a limitation on the image size? Microscopy images are
>     huge, about 30.000 x 30.000 pixels.
>
>     2) Is there a limitation on the number of slides? Given the large
>     image size, 3DSlicer might run out of memory at one moment in time.
>     I would need 300 to 600.
>
>     3) How can I build a 3D stack from TIF or JPEG images? Do I need to
>     convert them first into a different format like NRRD, or can I just
>     load them? Any suggestion for convertion tools?
>
>     Thanks a lot!
>     Holger
>
>
>
>
> --
> Holger Lange, Ph.D.
> CTO Flagship Bioscience
> www.flagshipbio.com <http://www.flagshipbio.com/>
>
> Germany - DE-32130 Enger - Bahnhofstr. 53 - +49 (0)5224 9776168
>
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