Stitching plugin cannot find TIFF files

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Stitching plugin cannot find TIFF files

jdavisknow
I will be stitching 2x2 images 7 slices in depth for 3 channels when I can
get the stitching plugin to find my files, but I am having trouble right out
of the gate because FIJI cannot find the TIFF files that I have exported
from Leica. I receive the following error log:

Loading (0, 0): C:\Users\user\Desktop\619e top section DIC\tile_01.tif ...
ERROR: Cannot find file: 'C:\Users\user\Desktop\619e top section
DIC\tile_01.tif' - abort stitching.
ERROR: Error during tile discovery, or invalid grid type. Aborting.

How can I resolve this first step? Is there a good tutorial for stitching
multi channel z-stacks somewhere?



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Re: Stitching plugin cannot find TIFF files

feelc
Hi,
Have you tried placing the images in a folder without whitespaces?
Try with a pair of them to rule out that possible issue.
Best,
Felipe

On Mon, 2 Dec 2019 at 20:44, jdavisknow <[hidden email]>
wrote:

> I will be stitching 2x2 images 7 slices in depth for 3 channels when I can
> get the stitching plugin to find my files, but I am having trouble right
> out
> of the gate because FIJI cannot find the TIFF files that I have exported
> from Leica. I receive the following error log:
>
> Loading (0, 0): C:\Users\user\Desktop\619e top section DIC\tile_01.tif ...
> ERROR: Cannot find file: 'C:\Users\user\Desktop\619e top section
> DIC\tile_01.tif' - abort stitching.
> ERROR: Error during tile discovery, or invalid grid type. Aborting.
>
> How can I resolve this first step? Is there a good tutorial for stitching
> multi channel z-stacks somewhere?
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

Stephan.Preibisch@mdc-berlin.de
Hi, please try using / or \\ instead of \ on Windows...

Best,
Stephan

Sent from my iPhone

> On Dec 2, 2019, at 16:49, Felipe Contreras <[hidden email]> wrote:
>
> Hi,
> Have you tried placing the images in a folder without whitespaces?
> Try with a pair of them to rule out that possible issue.
> Best,
> Felipe
>
>> On Mon, 2 Dec 2019 at 20:44, jdavisknow <[hidden email]>
>> wrote:
>>
>> I will be stitching 2x2 images 7 slices in depth for 3 channels when I can
>> get the stitching plugin to find my files, but I am having trouble right
>> out
>> of the gate because FIJI cannot find the TIFF files that I have exported
>> from Leica. I receive the following error log:
>>
>> Loading (0, 0): C:\Users\user\Desktop\619e top section DIC\tile_01.tif ...
>> ERROR: Cannot find file: 'C:\Users\user\Desktop\619e top section
>> DIC\tile_01.tif' - abort stitching.
>> ERROR: Error during tile discovery, or invalid grid type. Aborting.
>>
>> How can I resolve this first step? Is there a good tutorial for stitching
>> multi channel z-stacks somewhere?
>>
>>
>>
>> --
>> Sent from: http://imagej.1557.x6.nabble.com/
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

jdavisknow
Thank you feelc and Stephen for your suggestions. I have tried both without
luck so far.

I have edited out white spaces in my folder name. I then launched the
Stitching plugin, browsed for my folder, and replaced \ with \\ in the
"Directory" box. I have also tried to replace \ with //.
<http://imagej.1557.x6.nabble.com/file/t382475/Stitching_parameters.png>
The log shows that FIJI appears to still be searching for the folder using
/.
<http://imagej.1557.x6.nabble.com/file/t382475/Stitching_log.png>
Is there another method of editing the search pathway?



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

Stein Rørvik
On Windows, you need to use either double backslashes \\ or single forward slashes / in filepaths. The latter is much safer, as the double backslashes might need to be duplicated as four slashes if the string is passed further on inside the plugin, because \\ is translated to \ so you need \\\\ to let it being passed internally as \\. Using single forward slashes avoids this problem and therefore nearly always work.

Stein

-----Original Message-----

Sent: 04. desember 2019 17:13
To: [hidden email]
Subject: Re: [ext] Re: Stitching plugin cannot find TIFF files

Thank you feelc and Stephen for your suggestions. I have tried both without luck so far.

I have edited out white spaces in my folder name. I then launched the Stitching plugin, browsed for my folder, and replaced \ with \\ in the "Directory" box. I have also tried to replace \ with //.

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

jdavisknow
Thank you Stein. I have tried editing the search path to include / instead of
\ within the Stitching plugin "Directory" field, but I continue to receive
'error during tile discovery' message. The log indicates that despite my
edits, it is still using \. Is there another field that I should edit?
<http://imagej.1557.x6.nabble.com/file/t382475/Stitching_parameters_ii.png>
<http://imagej.1557.x6.nabble.com/file/t382475/Stitching_log.png>



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

Stein Rørvik
It seems like you are doing everything correctly, so I don't understand why it does not work. I just tried it myself and it works out-of-the-box both with single forward and single backslashes, and also spaces in the path, so that should not be the reason.

Are you sure you have typed the filename template correctly, with the correct number of digits and no whitespace after the .tif extension? If your files are named e.g. myfile_001.tif you must use myfile_{iii}.tif as the template name.

Stein

-----Original Message-----
Sent: 5. desember 2019 19:27
To: [hidden email]
Subject: Re: [ext] Re: Stitching plugin cannot find TIFF files

Thank you Stein. I have tried editing the search path to include / instead of \ within the Stitching plugin "Directory" field, but I continue to receive 'error during tile discovery' message. The log indicates that despite my edits, it is still using \. Is there another field that I should edit?

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

jdavisknow
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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