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-tp5022734p5022765.html

The auto numbering that LAS X performs is somewhat more complex than what you
have outlined. My files end up as myfile_TileScan_619e_s00_z00_RAW_ch02,
myfile_TileScan_619e_s01_z00_RAW_ch02,
myfile_TileScan_619e_s02_z00_RAW_ch02, ect. I tried to edit tile name from
myfile_{ii}.tif to myfile_{xxxi} to account for all the characters that LAS
X uses in its naming scheme. I then tried changing the files names a number
of different ways to see if they would be recognized, but nothing was
successful. Do I need to manually rename all my files? I have 2x2 tiles at 7
slices for 3 channels that I would like to merge using the same positioning,
so do you have advice on how to rename such that the plugin understands all
of those parameters?

A friend recommended that I skip trying to tell the plugin about positioning
and just use “unknown position” for type in the initial Grid/collection
stitching popup. This allows the plugin to find files, but it compresses all
the slices and all the channels into a single image (all nicely stitched it
appears). Is there a good tutorial somewhere on how to effectively use this
plugin?




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