Posted by
Majurski, Michael Paul (Fed) on
URL: http://imagej.273.s1.nabble.com/reUse-Grid-stitching-generated-coords-tp5014013p5014017.html
Jason,
MIST only handles grids of 2D images.
It can handle a series of independent Z planes, registering each z plane independently using the timeslices functionality (treating the Z planes as different time slices), but it cannot register a volume of images.
Thanks
~Michael Majurski
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Jason Miller
Sent: Thursday, August 13, 2015 1:45 PM
To:
[hidden email]
Subject: Re: reUse Grid stitching generated coords
Hi Michael-
I know I am just confirming information that you have already provided on your excellent webpage describing MIST, but we can't use MIST to force exact stitching from a configuration file is the images to be stitched are 3d instead of 2d, correct?
Thanks so much
-Jason
-------
Jason Miller, MD, PhD
University of Michigan Kellogg Eye Center
Home address:
117 Worden Ave
Ann Arbor, MI 48103
Cell: (415) 225-2134
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On Thu, Aug 13, 2015 at 1:06 PM, Majurski, Michael Paul <
[hidden email]> wrote:
> Simone,
>
> I do not know how to force the "Grid/Collection" stitching plugin to
> use a specific set of positions to assemble a new channel. As far as I
> understand it, using the positions from file gives the stitching tool
> a starting point from which to optimize translations.
>
> However, I can add a plug for the stitching plugin we developed which
> I know can use coordinates generated on a previous stitching run to
> assemble a stitched image from new images. This seems to follow your
> use case of using a single channel to register the images, and then
> assemble stitched images from the other channels using those exact image positions.
>
> The stitching plugin:
>
https://github.com/NIST-ISG/MIST>
> Install Guide:
>
https://github.com/NIST-ISG/MIST/wiki/Install-Guide>
> The FAQ about stitching secondary channels.
>
https://github.com/NIST-ISG/MIST/wiki/FAQ#how-to-stitch-from-metadata>
https://github.com/NIST-ISG/MIST/wiki/FAQ#stitching-multiple-channels>
> Thanks,
> ~The NIST ISG Team
> ~Michael Majurski
>
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of
> simone codeluppi
> Sent: Thursday, August 13, 2015 10:58 AM
> To:
[hidden email]
> Subject: reUse Grid stitching generated coords
>
> Hi
> My goal is to stitch a multi-channels image using the coordinates or
> overlapping of the tiles generated in the stitching of a reference
> channel (ex. DAPI staining). I first run the plugin stitching the
> Reference channel (grid setting) saving the TileConfiguration or
> TileConfiguration.registered file. I then I re-run the plugin on a
> different channel using the "Position from file" setting from
> TileConfiguration or TileConfiguration.registered but the stitching result is slightly different. Is there a way to "force"
> the plugin to place the tiles using the previously generated coord?
>
> Any help will be greatly appreciated.
> Thanks a lot!
>
> Simone
>
>
>
>
>
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