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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[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/
>
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>

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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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[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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[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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[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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[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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[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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[Stein Rørvik]

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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[CARL Philippe (LBP)]

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 : [phone]

----- 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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[jdavisknow]

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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