Re: [ext] Re: Stitching plugin cannot find TIFF files

Posted by jdavisknow on
URL: http://imagej.273.s1.nabble.com/Stitching-plugin-cannot-find-TIFF-files-tp5022734p5022795.html

Thank you Philippe and Stein, now that I've handed in grades for my students
I've been able to make some progress on stitching.

Renaming the files and using Stitch Sequence of Grids of Images is getting
me close to where I need to be. I had hoped that the plugin would stitch my
first z series (DIC channel) then position the subsequent z series (Alexa
488 and Alexa 568) based on this. My stitching results do not seem to bear
this out, however. One of my channels produces two tiles with signal and two
tiles with no signal, but I still expect a 2x2 stitched field. The resulting
image is only half the width of the stitched images from channels with
signal in all tiles, so a) positioning is not based on the first z series
and b) the plugin is not handling images with no signal well.

"Stitch Multiple Series or Tile Scan File" of the original Lif files does
seem to stitch channels 2 and 3 based on channel 1, but is there a way to
separate the merged colors to allow quantification?



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