http://imagej.273.s1.nabble.com/How-does-Multiview-Reconstruction-compare-to-Zeiss-tp5010290p5010304.html
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
> 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.htmlDr. David Knecht