Posted by
Jan Eglinger-3 on
Jun 15, 2011; 12:47pm
URL: http://imagej.273.s1.nabble.com/Opening-Mosaix-zvi-files-with-Bio-Formats-tp3684230p3684231.html
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.
> 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. 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?
Thanks for your help,
Jan