Problem using stitching plugin

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Problem using stitching plugin

Eric Leroy-2
Hi,

I am trying to use the Grid/Collection stitching plugin. My images are
called image-1-1.tif, image-1-2.tif and so on. I defined as pattern for
the file names for tiles the string image-{x}-{y}.tif and I have an error
message saying that it can not load the file image-{x}-{y}.tif. Can you
tell me where is the problem, I searched in the Fiji website but I didn't
found documentation for the syntax that should be used.
Thank you for your help

Regards,
--
Eric Leroy
Responsable de la plateforme microscopie électronique
Institut de Chimie et des Matériaux Paris Est
UMR 7182 - CNRS - UPEC
2/8, rue Henri Dunant
94320 THIAIS
Tel : (33-1) 49 78 12 09
Fax : (33-1) 49 78 12 03

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Re: Problem using stitching plugin

Stephan Preibisch
Hi Eric,

did you choose the right type of grid/collection? And the right parameters, which ones did you use, how are all the files called? Also can you provide the precise error, exception and log as shown by the plugin? Without this information it is really hard for me to say anything ...

Cheers, Stephan

On Apr 9, 2014 7:31 PM, Eric Leroy <[hidden email]> wrote:
>
> Hi,
>
> I am trying to use the Grid/Collection stitching plugin. My images are
> called i

mage-1-1.tif, image-1-2.tif and so on. I defined as pattern for > the file names for tiles the string image-{x}-{y}.tif and I have an error > message saying that it can not load the file image-{x}-{y}.tif. Can you > tell me where is the problem, I searched in the Fiji website but I didn't > found documentation for the syntax that should be used. > Thank you for your help > > Regards, > -- > Eric Leroy > Responsable de la plateforme microscopie électronique > Institut de Chimie et des Matériaux Paris Est > UMR 7182 - CNRS - UPEC > 2/8, rue Henri Dunant > 94320 THIAIS > Tel : (33-1) 49 78 12 09 > Fax : (33-1) 49 78 12 03 > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Re: Problem using stitching plugin

Mark Hiner-2
Hi Eric,

 Because the wildcards for image indices ({x} and {y}) are present in your
output, it looks like they were not processed by the type of
grid/collection stitching you were running.

 I am assuming you looked at this fiji wiki entry
<http://fiji.sc/Stitching>for example syntax, which only mentions
using {x} and {y}. However, the
wildcards you can use actually depends on which type of grid/collection
stitching you choose.

 For the various "Grid: ..." entries, you can only have one {i} wildcard
position.
 For "Filename defined position", you can have an {x} and {y}.. so I'm
assuming this is what you want to use.

If you were using "Filename defined position" and got that error, it's
definitely a bug and please let us know.

In the mean time I will edit that wiki page to more fully explain when to
use each wildcard.

Thanks!
Mark


On Wed, Apr 9, 2014 at 5:28 AM, Stephan Preibisch <[hidden email]>wrote:

> Hi Eric,
>
> did you choose the right type of grid/collection? And the right
> parameters, which ones did you use, how are all the files called? Also can
> you provide the precise error, exception and log as shown by the plugin?
> Without this information it is really hard for me to say anything ...
>
> Cheers, Stephan
>
> On Apr 9, 2014 7:31 PM, Eric Leroy <[hidden email]> wrote:
> >
> > Hi,
> >
> > I am trying to use the Grid/Collection stitching plugin. My images are
> > called i
>
> mage-1-1.tif, image-1-2.tif and so on. I defined as pattern for > the file
> names for tiles the string image-{x}-{y}.tif and I have an error > message
> saying that it can not load the file image-{x}-{y}.tif. Can you > tell me
> where is the problem, I searched in the Fiji website but I didn't > found
> documentation for the syntax that should be used. > Thank you for your help
> > > Regards, > -- > Eric Leroy > Responsable de la plateforme microscopie
> électronique > Institut de Chimie et des Matériaux Paris Est > UMR 7182 -
> CNRS - UPEC > 2/8, rue Henri Dunant > 94320 THIAIS > Tel : (33-1) 49 78 12
> 09 > Fax : (33-1) 49 78 12 03 > > -- > ImageJ mailing list:
> http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Problem using stitching plugin

Mark Hiner-2
>
> which only mentions using {x} and {y}. However, the wildcards you can use
> actually depends on which type of grid/collection stitching you choose.
>

Actually, I'm wrong.. the page appropriately differentiates the two
wildcard situations already!


On Wed, Apr 9, 2014 at 7:43 AM, Mark Hiner <[hidden email]> wrote:

> Hi Eric,
>
>  Because the wildcards for image indices ({x} and {y}) are present in your
> output, it looks like they were not processed by the type of
> grid/collection stitching you were running.
>
>  I am assuming you looked at this fiji wiki entry<http://fiji.sc/Stitching>for example syntax, which only mentions using {x} and {y}. However, the
> wildcards you can use actually depends on which type of grid/collection
> stitching you choose.
>
>  For the various "Grid: ..." entries, you can only have one {i} wildcard
> position.
>  For "Filename defined position", you can have an {x} and {y}.. so I'm
> assuming this is what you want to use.
>
> If you were using "Filename defined position" and got that error, it's
> definitely a bug and please let us know.
>
> In the mean time I will edit that wiki page to more fully explain when to
> use each wildcard.
>
> Thanks!
> Mark
>
>
> On Wed, Apr 9, 2014 at 5:28 AM, Stephan Preibisch <[hidden email]>wrote:
>
>> Hi Eric,
>>
>> did you choose the right type of grid/collection? And the right
>> parameters, which ones did you use, how are all the files called? Also can
>> you provide the precise error, exception and log as shown by the plugin?
>> Without this information it is really hard for me to say anything ...
>>
>> Cheers, Stephan
>>
>> On Apr 9, 2014 7:31 PM, Eric Leroy <[hidden email]> wrote:
>> >
>> > Hi,
>> >
>> > I am trying to use the Grid/Collection stitching plugin. My images are
>> > called i
>>
>> mage-1-1.tif, image-1-2.tif and so on. I defined as pattern for > the
>> file names for tiles the string image-{x}-{y}.tif and I have an error >
>> message saying that it can not load the file image-{x}-{y}.tif. Can you >
>> tell me where is the problem, I searched in the Fiji website but I didn't >
>> found documentation for the syntax that should be used. > Thank you for
>> your help > > Regards, > -- > Eric Leroy > Responsable de la plateforme
>> microscopie électronique > Institut de Chimie et des Matériaux Paris Est >
>> UMR 7182 - CNRS - UPEC > 2/8, rue Henri Dunant > 94320 THIAIS > Tel :
>> (33-1) 49 78 12 09 > Fax : (33-1) 49 78 12 03 > > -- > ImageJ mailing list:
>> http://imagej.nih.gov/ij/list.html
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>

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Re: Problem using stitching plugin

Eric Leroy-2
In reply to this post by Eric Leroy-2
Hi,

Thank you, you were right I didn't used the correct option.

Now it works ! Thank you again

Regards
Eric

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