Posted by
Daniel James White on
Jun 15, 2011; 3:21pm
URL: http://imagej.273.s1.nabble.com/Opening-Mosaix-zvi-files-with-Bio-Formats-tp3684230p3684235.html
Hi Jan,
On Jun 15, 2011, at 4:55 PM, Jan Eglinger wrote:
> Hi Dan,
>
> thanks for your comments, I'll retry with images using some overlap.
> However, the results I got with just a well aligned camera and without
> stitching calculations - although not yielding perfect images - _were_
> indeed sufficient for my purpose.
> And now I'd like to be able to work with those images containing 0% overlap.
you can do it, but remember that the plugin is expecting overlap
to be able to optimize the tile positions..
but it will in any case read the stage position to get the first initial guess..
which for you might be close enough.
>
> On 15.06.2011 4:21 PM, Daniel James White wrote:
>> On Jun 15, 2011, at 3:16 PM, Jan Eglinger wrote:
>>> 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?
>
> In AxioVision, a file acquired with Mosaix mode but not processed by the
> built-in Stitching will be opened as a full X*Y tiled image (with the
> tile borders possibly visible due to imperfect illumination and lens
> aberrations) ...
right....
but thats just eye candy... so you can "see" an overview.
... but there is no good reason for actually destructively saving the images like that.
The real image info is the individual tiles, and thats what Zeiss gives us. ...
We versatility in how to handle the tiles...
not some poorly stitched and then impossible to fix single overview image...
In the general case, the tile images need to be accessible individually - would you agree?
In your case you want to get straight to the roughly stitched overview image.... that has "zero" overlap and ugly edges.
Presently imageJ has no way to do that automagically: using the stage positions to make a rough tile view.
If you want to write an extension to bio-formats importer that does that pre processing on file import,
and spits the roughly splatted together overview image into an imageJ window,
then its for sure possible... feel free to implement it.
But the general case is that tiles should have overlap, and should be stitched properly according to the overlapping info close to the edges
as this output is then suitable for measurement and segmentation, whereas the rough splatted together image is not.
>
>>
>> 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?
>
> ... and older versions of Bio-Formats used to open those files in
> exactly that same way, hence my very first mail in this thread.
Yes, we changed it as it was inconsistent with the way Zeiss .lsm files are handled,
which also have tile scan s that need to be stitched... as does any tile scan from a system that can do mosaic/tile-scans.
Remember we are trying to make the whole of Fiji work using sensible defaults
that cover most cases, but still allow edge cases (like zero overlap) to be doable.
Most folks are doing a 10% or so overlap, as thats a sensible thing to do in most cases:
so you dont miss some parts at the edges, and also so that the stitching algorithms can work.
The stage position info is in the metadata an dis read by bio-formats,
so you can assemble the roughly stitched image overview any way you like from that info.
It could be another plugin in the stitching menu:
Stitch roughly using stage position data only.
Fast but ugly... but maybe sometimes good enough, as in your case.
Or you can just export the roughly stitched image from Axiovision.... maybe.
cheers
Dan
>
> Best,
> 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
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