Some questions about the calibration of 16-bit image. Thank you

[Zhenyu Shou]

Dear All:

 I have ImageJ 1.37 version installed in my Windows computer. I just found
out that I was NOT allowed to calibrate 16-bit image. I was told that only
8-bit image can be calibrated.

 (1). I want to confirm if it is true for current version of ImageJ.

 (2). If it is true, I am wondering if I can download some plugins or
patches so that I can calibrate 16-bit images.

 Thank you and have a good weekend!


----------------------------------------------------------------------
Zhenyu Shou, Ph.D
Radiation Oncology Physicist
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[Wayne Rasband]

I found this in the release notes  
(http://rsb.info.nih.gov/ij/notes.html):

     v1.38a, 27 October 2006
         - Analyze/Calibrate has better support for 16-bit images.

-wayne


On Dec 8, 2006, at 11:26 AM, Zhenyu Shou wrote:

> Dear All:
>
>  I have ImageJ 1.37 version installed in my Windows computer. I just  
> found
> out that I was NOT allowed to calibrate 16-bit image. I was told that  
> only
> 8-bit image can be calibrated.
>
>  (1). I want to confirm if it is true for current version of ImageJ.
>
>  (2). If it is true, I am wondering if I can download some plugins or
> patches so that I can calibrate 16-bit images.
>
>  Thank you and have a good weekend!
>
>
> ----------------------------------------------------------------------
> Zhenyu Shou, Ph.D
> Radiation Oncology Physicist
> -----------------------------------------------------------------------
> ---
>

[Rainer Kohler]

Hi,

I have a time series of image stacks with three channels from
FluoView. Size 1 GB.
How can I project the z-stacks to create a time series of the
projections of merged images as well as of the separate channels.
Because of memory restrictions it seems not to work in FluoView.
Could I do it in ImageJ?


Thanks
Rainer





--
Rainer Kohler, Ph.D
Microscopist
Center for Molecular Imaging Research
Massachusetts General Hospital/ Harvard Medical School
Building 149, 13th  Street, Room 5406
Charlestown, MA 02129-2060
Tel. [phone]
[hidden email]

[Albert Cardona]

Assuming each stack is a time point, it's easy:
For each stack:
1 - separate channels
2 - Z-project

If you want to browse the 4D series as RGB and do single-channel
Z-projections:
1 - save each stack as an image sequence (a loop in a macro will do,
don't do it manually!)
2 - open all images from all stacks as a virtual stack with the Virtual
Stack Opener
3 - do Z projections (available in the ImageJ plugins site)
4 - collect all Z projections in a stack
5 - split channels of the Z-projections stack

Voilà.

Albert

[Joachim Walter]

You can use the Image5D plugin.
- If you have your data as separate 2D TIFF images all in one directory,
you open them with the Virtual Image5D opener.
- Click on the "Color" button and assign a color to each channel (not
limited to RGB)
- Use "Z Project" of the Image5D plugins. In the window that pops up you
have to select "All Time Frames".
The resulting series of projections has to fit in memory, though.

Good Luck,
Joachim



Rainer Kohler schrieb:

> Hi,
>
> I have a time series of image stacks with three channels from
> FluoView. Size 1 GB.
> How can I project the z-stacks to create a time series of the
> projections of merged images as well as of the separate channels.
> Because of memory restrictions it seems not to work in FluoView.
> Could I do it in ImageJ?
>
>
> Thanks
> Rainer
>
>
>
>
>

--
------------------------------------------------------------------
  Dr. Joachim Walter
  Till I.D. GmbH
  c\o BioImaging Zentrum
  Großhaderner Str. 2
  82152 Martinsried, Germany

  Tel.: [phone]
  Fax:  [phone]

  [hidden email]
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