Hi All -
I have a question about integrating Micro-Manager acquisition with the
Grid/Collection stitching plugin, so I'm crossposting to both the
Micro-Manager and ImageJ lists. I have a user who wants to do the following:
In a time lapse, acquire a set of tiling positions covering multiple
separate objects, and then stitch the individual fields together
separately. The samples are zebrafish, which are spaced a few
millimeters apart in a dish, and we want to acquire a set of ~4
overlapping images covering the structure of interest in each zebrafish.
It's easy to acquire this data in Micro-manager by specifying the set of
positions for each fish, but when we go to stitch it together using the
Grid/Collection plugin using the coordinates in the metadata, of course
it includes the large amount of dark space between the images, which is
inconvenient.
What I would like to do is to split up the OME TIFF stack from
micro-manager into sets of positions corresponding to individual fish,
and then stitch each set separately. I have micro-manager save each
position to a separate file, but even if I try to just stitch one set of
these files, the metadata includes information about all the positions
that were acquired and it still adds a great deal of dark space.
Does anyone know of a way to split an OME-TIFF stack so that the
metadata is rewritten to contain only the positions in the current
subset of the stack? I'd like to be able to acquire all my positions,
and then run a script so that, e.g., positions 1-3 are saved to one
stack that can be stitched, positions 4-6 to another, etc.
Thanks,
Kurt
--
Kurt Thorn
Director, Nikon Imaging Center
http://nic.ucsf.edu/blog/--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html
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