Re: Opening Mosaix zvi files with Bio-Formats

Posted by Daniel James White on Jun 15, 2011; 2:29pm
URL: http://imagej.273.s1.nabble.com/Opening-Mosaix-zvi-files-with-Bio-Formats-tp3684230p3684236.html

Hi Jan,

On Jun 15, 2011, at 2:47 PM, Jan Eglinger wrote:

> Hi Dan,
>
> thanks for your reply.
>
> On 15.06.2011 8:59 AM, Daniel James White wrote:
>> We asked for the change in behaviour to make it consistent with how
>> tile scans from the Zeiss LSM 7xx come our as single .lsm files.
>
> I see. In my case, all mosaic positions are saved in a single zvi file.
> What's the best way to open these now? Whould I open all 64 series (in
> case of an 8x8 mosaic) in separate windows and then stitch them using
> the plugin? The command "Stitch Grid of Images" takes a directory as
> input, but I have a single file only.

nope  - use the plugin:
Stitch multiple series or tile scan file

which takes a single file input.

>
>> This is so one can then use the stitching plugin:
>> Stitch multiple series or tile scan file
>> to stitch the images properly according to the stage positions,
>> fine tuning the overlap and blending of the edges,
>> so the result image is segmentable etc.
>>
>> The Zeiss stitching does not adjust the position of the tiles
>> and you can easily se the edges are not well matched,
>> esp when the camera is not perfectly square with the stage.
>>
>> So this is a feature indeed.
>>
>> Let us know if that plugin version can stitch your
>> axiovision .zvi mosaic scans.
>>
>
> 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.

it wil never be perfect enough, as the lenses never have perfectly flat and distortion free field of view,
and even a tiny camera rotation will show up over a large tile scan.

> In my experience, stitching algorithms don't help much
> in that case, and I simply want to put the tiles together with 0% overlap.

you will still have problems at the edges of the tiles,
they wil not line up quite right.

Best to have overlapping info and use that to align the tile correctly.

>
> How can I achieve this with the current plugin?

Use some overlap.. enough for the plugin to see enough of the same stuff in overlapping areas.

the images with no information will be ignored if you use the right settings.

why not try using multiple points instead of tile scan if the image is so sparse,
making sure there is overlap between the fields of view...?

Dan



>
> Thanks for your help,
> 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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Germany

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