Re: Opening Mosaix zvi files with Bio-Formats

Posted by Daniel James White on Jun 15, 2011; 2:21pm
URL: http://imagej.273.s1.nabble.com/Opening-Mosaix-zvi-files-with-Bio-Formats-tp3684230p3684233.html

Hi Jan,

On Jun 15, 2011, at 3:16 PM, Jan Eglinger wrote:

> Hi again,
>
> On 15.06.2011 2:47 PM, Jan Eglinger wrote:
>> In my case, the image data contains 90% black area and only very few
>> elongated objects. That's why I have to rely on a good alignment of
>> camera and stage. In my experience, stitching algorithms don't help much
>> in that case, and I simply want to put the tiles together with 0% overlap.
>>
>> How can I achieve this with the current plugin?
>
> Please excuse my slightly premature question. I now found that I can
> open the mosaic file using "Stitch Multiple Series or Tile Scan File",
> then unchecking "Compute overlap", setting the overlap to 0% and the
> Fusion Method to "None".

Good, that how it should work!!!

>
> However, this opens my 2-channel stack in RGB mode, thereby consuming an
> unnecessary amount of memory.

Yes, and if its a 4 channel image... we are in trouble!

so Steffi and I talked about the need to use composite image instead of RGB,
so you can have many more "channels"

>
> Any hint how I can directly open as 2-channel hyperstack?

split them, then merge as a composite
throw away the empty channel....
i guess a script would be needed to make that efficient.

>
> In my opinion, it would be nice to have an intuitive way to open this
> kind of zvi file just as the acquisition software, i.e. AxioVision, does.

how do you mean exactly?

This is a job for the bio-formats importer.....
which maybe you can suggest how you might like it to be able to work as an option?

Dan



>
> Cheers,
> Jan

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
[phone] (Work phone at MPI-CBG)
[phone] (Fax MPI-CBG LMF)

http://www.bioimagexd.net  BioImageXD
http://pacific.mpi-cbg.de                Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk                Dan's Homepages
https://ifn.mpi-cbg.de  Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )