measuring intensity quantiles

[Jan Eglinger-5]

Dear all,

is there a quick way to measure the 90-percent quantile of intensity
within an ROI (instead of just the Mean, Min or Max) ?

Thanks for your help,
jan

--
Jan Eglinger
PhD Student, Eckhard Lammert group
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 Dresden
Germany

[Harry Parker]

Hi Jan,

Yes, you can easily create a macro using the getHistogram function using 4 bins.
See the documentation and example macros at
    http://rsb.info.nih.gov/ij/developer/macro/functions.html#G
(You must convert the image to a 16 bit or float type first for this to work.)
 
--  
Harry Parker  
Senior Systems Engineer  
Digital Imaging Systems, Inc.

----- Original Message ----
From: Jan Eglinger <[hidden email]>
To: [hidden email]
Sent: Wednesday, February 20, 2008 10:51:05 AM
Subject: measuring intensity quantiles

Dear
all,

is
there
a
quick
way
to
measure
the
90-percent
quantile
of
intensity
within
an
ROI
(instead
of
just
the
Mean,
Min
or
Max)
?

Thanks
for
your
help,
jan

--
Jan
Eglinger
PhD
Student,
Eckhard
Lammert
group
Max
Planck
Institute
of
Molecular
Cell
Biology
and
Genetics
Pfotenhauerstrasse
108
01307
Dresden
Germany





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[Yan Gao]

Image J,

LOCI Bio-Formats importer plugin helped me opening a small svs Aperio
file.  Thanks Melissa Linkert and OMELOCI made me able to read svs file in
Image J.  Now I still have problem open a normal sized svs file.  Image J
has limited memory size.  I can not open 12 MB svs file in Image J.  Can
someone help me again on this issue?  Thank you very much.

 Yan
=====================================

Yan Gao,  Doctoral of Science,  HTL (ASCP)
Novartis Institutes for BioMedical Research
250 Massachusetts Avenue, Lab 4C-430-02
Cambridge, MA 02139



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[ctrueden]

Hi Yan,

LOCI Bio-Formats importer plugin helped me opening a small svs Aperio
> file.  Thanks Melissa Linkert and OMELOCI made me able to read svs file in
> Image J.  Now I still have problem open a normal sized svs file.  Image J
> has limited memory size.  I can not open 12 MB svs file in Image J.  Can
> someone help me again on this issue?  Thank you very much.
>

Rather than a memory issue, this is most likely a bug in the Bio-Formats SVS
support. SVS is a fairly sophisticated format, and we only have a few sample
files. If you could send us a non-working sample, it would be very helpful
in diagnosing and fixing your problem. If the file is less than 15 MB, you
can send it to me directly as an email attachment; otherwise if you need a
place to store the file I can give you our FTP server information off-list.

Thanks,
Curtis

On Wed, Feb 20, 2008 at 3:08 PM, Yan Gao <[hidden email]> wrote:

> Image J,
>
> LOCI Bio-Formats importer plugin helped me opening a small svs Aperio
> file.  Thanks Melissa Linkert and OMELOCI made me able to read svs file in
> Image J.  Now I still have problem open a normal sized svs file.  Image J
> has limited memory size.  I can not open 12 MB svs file in Image J.  Can
> someone help me again on this issue?  Thank you very much.
>
>  Yan
> =====================================
>
> Yan Gao,  Doctoral of Science,  HTL (ASCP)
> Novartis Institutes for BioMedical Research
> 250 Massachusetts Avenue, Lab 4C-430-02
> Cambridge, MA 02139
>
>
>
> _________________________
>
> CONFIDENTIALITY NOTICE
>
> The information contained in this e-mail message is intended only for the
> exclusive use of the individual or entity named above and may contain
> information that is privileged, confidential or exempt from disclosure
> under applicable law. If the reader of this message is not the intended
> recipient, or the employee or agent responsible for delivery of the
> message to the intended recipient, you are hereby notified that any
> dissemination, distribution or copying of this communication is strictly
> prohibited. If you have received this communication in error, please
> notify the sender immediately by e-mail and delete the material from any
> computer.  Thank you.
>