Posted by
Saalfeld, Stephan on
Nov 05, 2014; 1:50am
URL: http://imagej.273.s1.nabble.com/How-does-Multiview-Reconstruction-compare-to-Zeiss-tp5010290p5010305.html
Hi David,
ok, so t is equal for all frames at the same stack index. There are two
options:
1. You can use the stitching plugin and either automatically align and
stitch the stacks or directly render them using the coordinates that you
provide. The Wiki explains how to do this. This requires that each
individual stack has no spatial jitter, i.e. your microscope found the
exact same spot at each frame.
2. If your microscope isn't that precise and the stacks jitter, you
could import the stacks as explained in the earlier mail into TrakEM2
(but with the correct frame index). Then you could use TrakEM2's
multi-layer mosaic alignment to get everything montaged and aligned
jointly, in the x,y plane and across time.
Best,
Stephan
On Tue, 2014-11-04 at 18:24 +0000, Knecht, David wrote:
> The stacks were all collected at similar enough times that they all are essentially synchronous. I don’t want to track any spots, I just want a single stack to analyze further in which the I have registered the images using the overlap as you would do in Align Images. Dave
>
>
> On Nov 4, 2014, at 11:20 AM, Stephan Saalfeld <
[hidden email]> wrote:
>
> > If I understand you correctly, t is not overlapping, i.e., you would
> > like to create a time series that shows when different spots were
> > imaged?
> >
> > You could do this in TrakEM2. Save your images as a series if TIF
> > files, generate an import.txt file with one row per frame in the format:
> >
> > <frame_file_name> <x_position> <y_position> <t_position>
> >
> > e.g.
> >
> > frame_x000y000t000.tif 0 0 0
> > frame_x000y000t001.tif 0 0 1
> > frame_x000y000t002.tif 0 0 2
> >
> > ...
> >
> > frame_x001y000t000.tif 1000 0 100
> > frame_x001y000t001.tif 1000 0 101
> > frame_x001y000t002.tif 1000 0 102
> >
> > ...
> >
> > frame_x04y003t000.tif 4000 3000 2300
> > frame_x04y003t001.tif 4000 3000 2301
> > frame_x04y003t002.tif 4000 3000 2302
> >
> > ...
> >
> >
> > Excel or OpenOffice Calc are great tools to generate such import files.
> >
> > If I got your question wrong and t is the same for all stacks, use the
> > Stitching plugin:
> >
> >
http://fiji.sc/Image_Stitching> >
> >
> > Best,
> > Stephan
> >
> >
> > On Tue, 2014-11-04 at 15:29 +0000, Knecht, David wrote:
> >> I have a series of xyt stacks collected in micro-manager at overlapping xy positions. I want to assemble them into a single large stack with all positions. What is the best plugin to do that? Thanks- Dave
> >>
> >> Dr. David Knecht
> >> Professor of Molecular and Cell Biology
> >> Core Microscopy Facility Director
> >> University of Connecticut
> >> Storrs, CT 06269
> >> 860-486-2200
> >>
> >> --
> >> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
> Dr. David Knecht
> Professor of Molecular and Cell Biology
> Core Microscopy Facility Director
> University of Connecticut
> Storrs, CT 06269
> 860-486-2200
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html--
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