Posted by
CARL Philippe (LBP) on
URL: http://imagej.273.s1.nabble.com/Stitching-plugin-cannot-find-TIFF-files-tp5022734p5022767.html
Dear Jessica,
> Do I need to manually rename all my files?
In the case you need to do such a job under a Windows OS, I would recommand you to use the Total Commander (
https://www.ghisler.com) software.
It's a shareware that has a very powerful File>Multi-Rename_Tool... which will able you to do the job you are looking for.
You can test the rename hypothesis and once validated your test you can actually undo you renaming.
The software has as well a <File>Compare_By_Content... feature that able for example to compare two code files to figure out their differences.
Have a nice week-end.
Philippe
Philippe CARL
Laboratoire de Bioimagerie et Pathologies
UMR 7021 CNRS - Université de Strasbourg
Faculté de Pharmacie
74 route du Rhin
67401 ILLKIRCH
Tel : +33(0)3 68 85 41 84
----- Mail original -----
De: "jdavisknow" <
[hidden email]>
À: "imagej" <
[hidden email]>
Envoyé: Vendredi 6 Décembre 2019 22:13:28
Objet: 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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