Re: Assemble xyt overlap stacks

Posted by Saalfeld, Stephan on Nov 04, 2014; 4:20pm
URL: http://imagej.273.s1.nabble.com/How-does-Multiview-Reconstruction-compare-to-Zeiss-tp5010290p5010295.html

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

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