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

Posted by Stein Rørvik on Dec 07, 2019; 1:43am
URL: http://imagej.273.s1.nabble.com/Stitching-plugin-cannot-find-TIFF-files-tp5022734p5022766.html

Have you tried to use
"myfile_TileScan_619e_s{ii}_z00_RAW_ch02.tif" as the template ?

There is also a plugin "Stitch Sequence of Grids of Images" that uses a filename template like
"Tile_Z{zzz}_Y{yyy}_X{xxx}.lsm".

I think this is closer to what you want. In your case the template will be something like
"myfile_TileScan_619e_s{xx}_z{zz}_RAW_ch{yy}.tif".

Stein

-----Original Message-----
Sent: 6. desember 2019 22:13
To: [hidden email]
Subject: Re: [ext] Re: Stitching plugin cannot find TIFF files

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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