ZVI slices

[Thomas Lenoir]

Hello everyone,

I have written code for opening zvi files, but I get 12 slices of 8bit  
each in place of 6 slices of 16bit, does anybody know how to merge  
them to form 16bit images?
In ImageJ app it works as expected, when I open the zvi file it gives  
me 6 windows.

Thanks,
Thomas

[phm]

Hi Thomas,

Try this plugin it open a lot of microscope file formats as ZVI


http://www.loci.wisc.edu/ome/formats.html


Philippe

> Hello everyone,
>
> I have written code for opening zvi files, but I get 12 slices of 8bit
> each in place of 6 slices of 16bit, does anybody know how to merge
> them to form 16bit images?
> In ImageJ app it works as expected, when I open the zvi file it gives
> me 6 windows.
>
> Thanks,
> Thomas
>
>

--
Mailly Philippe, PhD
UMR 7101, CNRS
Univ. Pierre et Marie Curie
7 quai St Bernard, 75005, Paris
France
tel: [phone]
fax: [phone]

[ctrueden]

Hi Thomas,

Are you still using Bio-Formats to load the files? I'm surprised that
calling the API is giving you a different bit depth in the image.
Perhaps it is due to the way you are constructing your ImagePlus
object.

I recommend using loci.plugins.Util.openProcessor to extract
ImageProcessor objects using an IFormatReader. Then you can use the
ImageJ API on the ImageProcessors however you like as usual.

If all else fails, to analyze differences in behavior, you can step
through the source code of loci.plugins.Importer, which does most of
the setup for getting images into ImageJ via Bio-Formats.

If you need additional assistance, I would need to see your source code.

-Curtis

On Dec 16, 2007 9:37 AM, Thomas Lenoir <[hidden email]> wrote:

> Hello everyone,
>
> I have written code for opening zvi files, but I get 12 slices of 8bit
> each in place of 6 slices of 16bit, does anybody know how to merge
> them to form 16bit images?
> In ImageJ app it works as expected, when I open the zvi file it gives
> me 6 windows.
>
> Thanks,
> Thomas
>

[Thomas Lenoir]

Thanks all for your answers, using loci.plugins.Util.openProcessor  
gives me what I want (6 16bit slices and not 12 8bit slices). I was  
using loci.plugin.browser.ImagePlusWrapper before.

Thomas

Le 17 déc. 07 à 17:38, Curtis Rueden a écrit :

> Hi Thomas,
>
> Are you still using Bio-Formats to load the files? I'm surprised that
> calling the API is giving you a different bit depth in the image.
> Perhaps it is due to the way you are constructing your ImagePlus
> object.
>
> I recommend using loci.plugins.Util.openProcessor to extract
> ImageProcessor objects using an IFormatReader. Then you can use the
> ImageJ API on the ImageProcessors however you like as usual.
>
> If all else fails, to analyze differences in behavior, you can step
> through the source code of loci.plugins.Importer, which does most of
> the setup for getting images into ImageJ via Bio-Formats.
>
> If you need additional assistance, I would need to see your source  
> code.
>
> -Curtis
>
> On Dec 16, 2007 9:37 AM, Thomas Lenoir <thomaslenoir@club-
> internet.fr> wrote:
>> Hello everyone,
>>
>> I have written code for opening zvi files, but I get 12 slices of  
>> 8bit
>> each in place of 6 slices of 16bit, does anybody know how to merge
>> them to form 16bit images?
>> In ImageJ app it works as expected, when I open the zvi file it gives
>> me 6 windows.
>>
>> Thanks,
>> Thomas
>>
>
>