loading single slices in stacks?

[Johan Henriksson]

Hello,
I am developing a 3D+time stack player and viewer. because the data set is
extremely big
it cannot all be loaded at once, nor can I split the files as it takes too
long (the viewer
has to be able to do quick previews).

so, I need the ability to load single slices from for example LSM files or
PICT stacks
without reading the entire file. is there a standard way of doing this?


--
------------------------------------------------
Johan Henriksson aka Mahogny aka Stålis
[hidden email] / [hidden email]
MSc Engineering
PhD student, Karolinska Institutet
http://www.areta.org
http://www.mtek.chalmers.se/~johen/

[Gabriel Landini]

On Monday 19 February 2007 13:08:18 Johan Henriksson wrote:

> Hello,
> I am developing a 3D+time stack player and viewer. because the data set is
> extremely big
> it cannot all be loaded at once, nor can I split the files as it takes too
> long (the viewer
> has to be able to do quick previews).
>
> so, I need the ability to load single slices from for example LSM files or
> PICT stacks
> without reading the entire file. is there a standard way of doing this?

There is a virtual stack opener plugin at the IJ site.
That may help.

Cheers.
G.

[ctrueden]

Hi Johan,

Bio-Formats (http://www.loci.wisc.edu/ome/formats.html) is capable of
reading individual slices from any of its supported formats. We use
this functionality in our 4D Data Browser plugin
(http://www.loci.wisc.edu/ome/browser.html) to achieve virtualization
functionality similar to the Virtual Stack Opener plugin, but with
configurable caching, and more supported formats.

-Curtis

On 2/19/07, Johan Henriksson <[hidden email]> wrote:

> Hello,
> I am developing a 3D+time stack player and viewer. because the data set is
> extremely big
> it cannot all be loaded at once, nor can I split the files as it takes too
> long (the viewer
> has to be able to do quick previews).
>
> so, I need the ability to load single slices from for example LSM files or
> PICT stacks
> without reading the entire file. is there a standard way of doing this?
>
>
> --
> ------------------------------------------------
> Johan Henriksson aka Mahogny aka Stålis
> [hidden email] / [hidden email]
> MSc Engineering
> PhD student, Karolinska Institutet
> http://www.areta.org
> http://www.mtek.chalmers.se/~johen/
>

... [show rest of quote]

[Katha Anki Reddy]

dear list

i am trying to find the size distribution of particles present in the my
image obtained from an experiemnt

is it possible to find the size distribution without thresholding ?


i found thresholding is a problem when we have the images like the one i
got

please let me know if there are anyways to do size distribution studies ?

i tried to attach that image, but mail bounced back because of attachment



thanks and regards

anki


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[Michael Schmid]

Hi Anki,

sometimes Process/Binary/Find Maxima with a suitable tolerance
value and output type "Maxima within Tolerance" can be better
than thresholding.

Michael
________________________________________________________________

On 20 Feb 2007, at 09:58, Katha Anki Reddy wrote:

> dear list
>
> i am trying to find the size distribution of particles present in  
> the my image obtained from an experiemnt
>
> is it possible to find the size distribution without thresholding ?
>
>
> i found thresholding is a problem when we have the images like the  
> one i got
>
> please let me know if there are anyways to do size distribution  
> studies ?
>
> i tried to attach that image, but mail bounced back because of  
> attachment
>
>
>
> thanks and regards
>
> anki
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.

... [show rest of quote]