Re: Opening Images from LSM

[Mario Emmenlauer-3]

Hi,

Oliver Braubach wrote:
> ImageJ says that they are at 16-bit?

well, it would be interesting to see if the lsm is indeed 8, 12 or 16 bit.
A simple test might be the filesize. Take
  x-resolution * y-resolution * slices * stacks,
that should be the rough filesize for 8 bit.
If your filesize is 3/2 of that, its 12 bit.
If your filesize is twice that, its 16 bit.

So for a single stack of 512 * 512 * 20 slices * 2 channels,
you should have 10485760 byte ~ 10MB for 8 bit, 15MB for
12 bit or 20MB for 16 bit.

Of course this only works if you have uncompressed lsm,
but mine are always uncompressed so chances are good.

 > Is there some resampling going on? Do I
> need to change this? Any insight would be most welcome.

If you have 12 or 16 bit, your monitor can only show you
8 bit of that. You can use the Brightness/Contrast setting
to change which 'region' of your dynamic range you want to
see. Or you can make a gamma-correction (0.5 or 0.4 should
be fine) to compress the dynamic range, then it will 'fit'
on your monitor.

Cheers,
   Mario

--
Mario Emmenlauer                             Phone: [phone]
Institute for Computer Science               Fax:   [phone]
Chair of Pattern Recognition and Image Processing
Albert-Ludwigs-University
Georges-Koehler-Allee 052, room 01-022
79110 Freiburg             mailto:emmenlau * informatik.uni-freiburg.de
Germany          http://lmb.informatik.uni-freiburg.de/people/emmenlau/

[Michael Doube-2]

Hi Oliver.  Open one of your images, hit [h] to get a histogram - the  
values should be spread out across the full range with a peak or two  
depending on the subject.  Then open image-> adjust-> brightness and  
contrast and adjust the max and min values to be just above and below  
your image data. hopefully this will make a difference- it's possible  
that imageJ's default windowing isn't working well for your images.

Good luck

Mike

Quoting Oliver Braubach <[hidden email]>:

> Hi
>
> I am having trouble viewing and processing Confocal Stacks (in LSM format,
> usually 8-bit) in ImageJ. The problem is that through being opened  
> with ImageJ
> individual slices in the stack become artificiallly overexposed, leaving them
> as nothing more but a lot of white and black - all the detail (gray) is lost.
> The images are fine when viewed in LSM image browser (Zeiss) and are  
>  not badly
> taken.
> ImageJ says that they are at 16-bit? Is there some resampling going on? Do I
> need to change this? Any insight would be most welcome.
> Thanks.
> Oliver
>

[OliverB]

Dear Michael

Thanks for you input regarding my ImageJ troubles.
I followed your suggestion and was able to overcome this problem.

Greetings from Canada
Oliver Braubach

Laboratory of Synaptic Function and Plasticity
Department of Physiology and Biophysics
Dalhousie University
Halifax, NS B3H 1X5 Canada
Tel: [phone]
Fax: [phone]




On Oct 27, 2007, at 7:12 AM, Michael Doube wrote:

> Hi Oliver.  Open one of your images, hit [h] to get a histogram -  
> the values should be spread out across the full range with a peak  
> or two depending on the subject.  Then open image-> adjust->  
> brightness and contrast and adjust the max and min values to be  
> just above and below your image data. hopefully this will make a  
> difference- it's possible that imageJ's default windowing isn't  
> working well for your images.
>
> Good luck
>
> Mike
>
> Quoting Oliver Braubach <[hidden email]>:
>
>> Hi
>>
>> I am having trouble viewing and processing Confocal Stacks (in LSM  
>> format,
>> usually 8-bit) in ImageJ. The problem is that through being  
>> opened  with ImageJ
>> individual slices in the stack become artificiallly overexposed,  
>> leaving them
>> as nothing more but a lot of white and black - all the detail  
>> (gray) is lost.
>> The images are fine when viewed in LSM image browser (Zeiss) and  
>> are  not badly
>> taken.
>> ImageJ says that they are at 16-bit? Is there some resampling  
>> going on? Do I
>> need to change this? Any insight would be most welcome.
>> Thanks.
>> Oliver
>>