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Problem with Grid/Collection stitching plugin

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Kurt Thorn

Problem with Grid/Collection stitching plugin

Hi All -

I'm trying to stitch a set of Z-stacks acquired in Micro-Manager using
the Grid/Collection stitching plugin in Fiji. Everything seems to work
OK except that the final stitched image is composed of repeated copies
of the first image stack in the set rather than stitching the actual
stacks at each position. However, the positions of these copies look
like they are in the correct place for the locations of the actual
tiles. Can anyone provide insight as to what may be going wrong? I've
attached the log file and can provide more information as needed.

Thanks,
Kurt

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Log.txt (41K) Download Attachment

ctrueden

Re: Problem with Grid/Collection stitching plugin

Hi Kurt,

> the final stitched image is composed of repeated copies of the first
> image stack

Grid/Collection stitching uses Bio-Formats to read the stage position
information as well as the pixels. If you run File > Import > Bio-Formats
and point it at your Micro-Manager .txt file, does it properly detect all
your stage positions? Do they open correctly individually? If not, this is
a Bio-Formats bug rather than a problem with the Stitching plugins.

Regards,
Curtis

On Thu, Oct 17, 2013 at 3:31 PM, Kurt Thorn <[hidden email]> wrote:

> Hi All -
>
> I'm trying to stitch a set of Z-stacks acquired in Micro-Manager using the
> Grid/Collection stitching plugin in Fiji. Everything seems to work OK
> except that the final stitched image is composed of repeated copies of the
> first image stack in the set rather than stitching the actual stacks at
> each position. However, the positions of these copies look like they are
> in the correct place for the locations of the actual tiles. Can anyone
> provide insight as to what may be going wrong? I've attached the log file
> and can provide more information as needed.
>
> Thanks,
> Kurt
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>

--
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Kurt Thorn

Re: Problem with Grid/Collection stitching plugin

On 10/17/2013 1:41 PM, Curtis Rueden wrote:

> Hi Kurt,
>
>> the final stitched image is composed of repeated copies of the first
>> image stack
> Grid/Collection stitching uses Bio-Formats to read the stage position
> information as well as the pixels. If you run File > Import > Bio-Formats
> and point it at your Micro-Manager .txt file, does it properly detect all
> your stage positions? Do they open correctly individually? If not, this is
> a Bio-Formats bug rather than a problem with the Stitching plugins.
>
> Regards,
> Curtis

I'm running grid/collection stitching with the Filename defined position
option, and pointing it to a folder of tif stacks with the naming
convention tumor_grid_animal04_2_MMStack_1-Pos_{xxx}_{yyy}.ome.tif and
the stitching plugin reports that it opens each stack separately, so I
think that's working OK? But perhaps it's a more subtle interaction
between BioFormats and the stitching plugin?

Thanks,
Kurt

>
> On Thu, Oct 17, 2013 at 3:31 PM, Kurt Thorn <[hidden email]> wrote:
>
>> Hi All -
>>
>> I'm trying to stitch a set of Z-stacks acquired in Micro-Manager using the
>> Grid/Collection stitching plugin in Fiji. Everything seems to work OK
>> except that the final stitched image is composed of repeated copies of the
>> first image stack in the set rather than stitching the actual stacks at
>> each position. However, the positions of these copies look like they are
>> in the correct place for the locations of the actual tiles. Can anyone
>> provide insight as to what may be going wrong? I've attached the log file
>> and can provide more information as needed.
>>
>> Thanks,
>> Kurt
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>

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Schebique

Re: Problem with Grid/Collection stitching plugin

Hi. I have noticed this behavior as well. It happen to me when trying to
stitch Leica tif tile files when .lei file is in the same folder and thus
files are read by Bioformats. I did not had a time to examine a problem
more deep.

Sincerely Schebique
Dne 17.10.2013 23:01 "Kurt Thorn" <[hidden email]> napsal(a):

> On 10/17/2013 1:41 PM, Curtis Rueden wrote:
>
>> Hi Kurt,
>>
>> the final stitched image is composed of repeated copies of the first
>>> image stack
>>>
>> Grid/Collection stitching uses Bio-Formats to read the stage position
>> information as well as the pixels. If you run File > Import > Bio-Formats
>> and point it at your Micro-Manager .txt file, does it properly detect all
>> your stage positions? Do they open correctly individually? If not, this is
>> a Bio-Formats bug rather than a problem with the Stitching plugins.
>>
>> Regards,
>> Curtis
>>
> I'm running grid/collection stitching with the Filename defined position
> option, and pointing it to a folder of tif stacks with the naming
> convention tumor_grid_animal04_2_MMStack_**1-Pos_{xxx}_{yyy}.ome.tif and
> the stitching plugin reports that it opens each stack separately, so I
> think that's working OK? But perhaps it's a more subtle interaction between
> BioFormats and the stitching plugin?
>
> Thanks,
> Kurt
>
>>
>> On Thu, Oct 17, 2013 at 3:31 PM, Kurt Thorn <[hidden email]> wrote:
>>
>> Hi All -
>>>
>>> I'm trying to stitch a set of Z-stacks acquired in Micro-Manager using
>>> the
>>> Grid/Collection stitching plugin in Fiji. Everything seems to work OK
>>> except that the final stitched image is composed of repeated copies of
>>> the
>>> first image stack in the set rather than stitching the actual stacks at
>>> each position. However, the positions of these copies look like they are
>>> in the correct place for the locations of the actual tiles. Can anyone
>>> provide insight as to what may be going wrong? I've attached the log file
>>> and can provide more information as needed.
>>>
>>> Thanks,
>>> Kurt
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.****html<http://imagej.nih.gov/ij/list.**html>
>>> <http://imagej.nih.gov/**ij/list.html<http://imagej.nih.gov/ij/list.html>
>>> >
>>>
>>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>
>>
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>

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ctrueden

Re: Problem with Grid/Collection stitching plugin

In reply to this post by Kurt Thorn

Hi Kurt,

> I'm running grid/collection stitching with the Filename defined
> position option, and pointing it to a folder of tif stacks with the
> naming convention
> tumor_grid_animal04_2_MMStack_1-Pos_{xxx}_{yyy}.ome.tif and the
> stitching plugin reports that it opens each stack separately, so I
> think that's working OK?

What happens if you select "Positions from file" for the Type, and "Defined
by image metadata" for the Order?

I will also reiterate my previous question:
> If you run File > Import > Bio-Formats and point it at your
> Micro-Manager .txt file, does it properly detect all your stage
> positions?

Regards,
Curtis

On Thu, Oct 17, 2013 at 4:01 PM, Kurt Thorn <[hidden email]> wrote:

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Kurt Thorn

Re: Problem with Grid/Collection stitching plugin

Hi Curtis -

On 10/18/2013 12:16 PM, Curtis Rueden wrote:

> Hi Kurt,
>
>> I'm running grid/collection stitching with the Filename defined
>> position option, and pointing it to a folder of tif stacks with the
>> naming convention
>> tumor_grid_animal04_2_MMStack_1-Pos_{xxx}_{yyy}.ome.tif and the
>> stitching plugin reports that it opens each stack separately, so I
>> think that's working OK?
> What happens if you select "Positions from file" for the Type, and "Defined
> by image metadata" for the Order?

This loads and stitches the images properly.
>
> I will also reiterate my previous question:
>> If you run File > Import > Bio-Formats and point it at your
>> Micro-Manager .txt file, does it properly detect all your stage
>> positions?

If I point it to the first ome.tif file, it brings up a dialog asking
for the positions I want to open. If I point it to the first
metadata.txt file, I get an error: Unknown file format.

Thanks for your help!

Kurt

> Regards,
> Curtis
>
>
> On Thu, Oct 17, 2013 at 4:01 PM, Kurt Thorn <[hidden email]> wrote:
>
>> On 10/17/2013 1:41 PM, Curtis Rueden wrote:
>>
>>> Hi Kurt,
>>>
>>> the final stitched image is composed of repeated copies of the first
>>>> image stack
>>>>
>>> Grid/Collection stitching uses Bio-Formats to read the stage position
>>> information as well as the pixels. If you run File > Import > Bio-Formats
>>> and point it at your Micro-Manager .txt file, does it properly detect all
>>> your stage positions? Do they open correctly individually? If not, this is
>>> a Bio-Formats bug rather than a problem with the Stitching plugins.
>>>
>>> Regards,
>>> Curtis
>>>
>> I'm running grid/collection stitching with the Filename defined position
>> option, and pointing it to a folder of tif stacks with the naming
>> convention tumor_grid_animal04_2_MMStack_**1-Pos_{xxx}_{yyy}.ome.tif and
>> the stitching plugin reports that it opens each stack separately, so I
>> think that's working OK? But perhaps it's a more subtle interaction between
>> BioFormats and the stitching plugin?
>>
>> Thanks,
>> Kurt
>>
>>> On Thu, Oct 17, 2013 at 3:31 PM, Kurt Thorn <[hidden email]> wrote:
>>>
>>> Hi All -
>>>> I'm trying to stitch a set of Z-stacks acquired in Micro-Manager using
>>>> the
>>>> Grid/Collection stitching plugin in Fiji. Everything seems to work OK
>>>> except that the final stitched image is composed of repeated copies of
>>>> the
>>>> first image stack in the set rather than stitching the actual stacks at
>>>> each position. However, the positions of these copies look like they are
>>>> in the correct place for the locations of the actual tiles. Can anyone
>>>> provide insight as to what may be going wrong? I've attached the log file
>>>> and can provide more information as needed.
>>>>
>>>> Thanks,
>>>> Kurt
>>>>
>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.****html<http://imagej.nih.gov/ij/list.**html>
>>>> <http://imagej.nih.gov/**ij/list.html<http://imagej.nih.gov/ij/list.html>
>>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>>
>>>
>>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>

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ctrueden

Re: Problem with Grid/Collection stitching plugin

In reply to this post by ctrueden

Hi Kurt,

> I just wanted to thank you with your help with getting this working.

You're very welcome! Glad to hear it is working.

I hope you do not mind me CCing the ImageJ and OME lists. People often ask
for help solving technical problems, but rarely share their success stories
publicly. It helps the morale of the team, as well as future funding, to
know that people find these tools useful.

> I just did some extensive testing and using the image metadata results
> in great stitching of Micro-Manager data. I'm impressed by the
> interoperability of all these different packages, which I guess owes a
> lot to Bioformats and the OME-TIFF file format.

There are many people who deserve thanks:

Stephan Preibisch did the hard work of authoring the stitching plugins.
http://fiji.sc/Stitching#Citation

Melissa Linkert, the primary Bio-Formats developer, implemented the
Micro-Manager reader, which makes extraction of the stage position metadata
possible.
http://openmicroscopy.org/site/about/licensing-attribution/citing-ome

Johannes Schindelin, the maintainer of Fiji, strives daily to ensure that
Fiji's various components remain compatible with one another.
http://fiji.sc/How_to_cite_Fiji%3F

The Micro-Manager team has done outstanding work and been very
collaborative.
http://www.micro-manager.org/wiki/Citing_Micro-Manager

The Open Microscopy Environment team maintains the OME-XML schema, which as
you point out is how the Stitching plugin can read stage position metadata
from so many different formats using Bio-Formats.
http://openmicroscopy.org/site/about/licensing-attribution/citing-ome

Continuing development of these projects would not be possible without the
efforts of the PIs, including Pavel Tomancak, Kevin Eliceiri and Jason
Swedlow. In particular, they organize invaluable "hackathons" where
developers get together to work on such interoperability. IIRC, it was at
one such event where Stephan made the Stitching plugins use Bio-Formats,
with the help of Melissa and myself.

Regards,
Curtis

On Wed, Oct 30, 2013 at 12:42 PM, Kurt Thorn <[hidden email]> wrote:

> Hi Curtis -
>
> I just wanted to thank you with your help with getting this working. I
> just did some extensive testing and using the image metadata results in
> great stitching of Micro-Manager data. I'm impressed by the
> interoperability of all these different packages, which I guess owes a lot
> to Bioformats and the OME-TIFF file format.
>
> Thanks,
> Kurt
>
>
> On 10/18/2013 12:16 PM, Curtis Rueden wrote:
>
>> Hi Kurt,
>>
>> I'm running grid/collection stitching with the Filename defined
>>> position option, and pointing it to a folder of tif stacks with the
>>> naming convention
>>> tumor_grid_animal04_2_MMStack_**1-Pos_{xxx}_{yyy}.ome.tif and the
>>> stitching plugin reports that it opens each stack separately, so I
>>> think that's working OK?
>>>
>> What happens if you select "Positions from file" for the Type, and
>> "Defined
>> by image metadata" for the Order?
>>
>> I will also reiterate my previous question:
>>
>>> If you run File > Import > Bio-Formats and point it at your
>>> Micro-Manager .txt file, does it properly detect all your stage
>>> positions?
>>>
>> Regards,
>> Curtis
>>
>>
>> On Thu, Oct 17, 2013 at 4:01 PM, Kurt Thorn <[hidden email]> wrote:
>>
>> On 10/17/2013 1:41 PM, Curtis Rueden wrote:
>>>
>>> Hi Kurt,
>>>>
>>>> the final stitched image is composed of repeated copies of the first
>>>>
>>>>> image stack
>>>>>
>>>>> Grid/Collection stitching uses Bio-Formats to read the stage position
>>>> information as well as the pixels. If you run File > Import >
>>>> Bio-Formats
>>>> and point it at your Micro-Manager .txt file, does it properly detect
>>>> all
>>>> your stage positions? Do they open correctly individually? If not, this
>>>> is
>>>> a Bio-Formats bug rather than a problem with the Stitching plugins.
>>>>
>>>> Regards,
>>>> Curtis
>>>>
>>>> I'm running grid/collection stitching with the Filename defined
>>> position
>>> option, and pointing it to a folder of tif stacks with the naming
>>> convention tumor_grid_animal04_2_MMStack_****1-Pos_{xxx}_{yyy}.ome.tif
>>> and
>>>
>>> the stitching plugin reports that it opens each stack separately, so I
>>> think that's working OK? But perhaps it's a more subtle interaction
>>> between
>>> BioFormats and the stitching plugin?
>>>
>>> Thanks,
>>> Kurt
>>>
>>> On Thu, Oct 17, 2013 at 3:31 PM, Kurt Thorn <[hidden email]>
>>>> wrote:
>>>>
>>>> Hi All -
>>>>
>>>>> I'm trying to stitch a set of Z-stacks acquired in Micro-Manager using
>>>>> the
>>>>> Grid/Collection stitching plugin in Fiji. Everything seems to work OK
>>>>> except that the final stitched image is composed of repeated copies of
>>>>> the
>>>>> first image stack in the set rather than stitching the actual stacks at
>>>>> each position. However, the positions of these copies look like they
>>>>> are
>>>>> in the correct place for the locations of the actual tiles. Can anyone
>>>>> provide insight as to what may be going wrong? I've attached the log
>>>>> file
>>>>> and can provide more information as needed.
>>>>>
>>>>> Thanks,
>>>>> Kurt
>>>>>
>>>>> --
>>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.******html<http://imagej.nih.gov/ij/list.****html>
>>>>> <http://imagej.nih.**gov/ij/list.**html<http://imagej.nih.gov/ij/list.**html>
>>>>> >
>>>>> <http://imagej.nih.gov/**ij/**list.html<http://imagej.nih.gov/**ij/list.html>
>>>>> <http://imagej.nih.**gov/ij/list.html<http://imagej.nih.gov/ij/list.html>
>>>>> >
>>>>> --
>>>>>
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.****html<http://imagej.nih.gov/ij/list.**html>
>>>> <http://imagej.nih.gov/**ij/list.html<http://imagej.nih.gov/ij/list.html>
>>>> >
>>>>
>>>>
>>>>
>>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.****html<http://imagej.nih.gov/ij/list.**html>
>>> <http://imagej.nih.gov/**ij/list.html<http://imagej.nih.gov/ij/list.html>
>>> >
>>>
>>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>
>>
>>
>
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Peter Blankenheim

Re: Problem with Grid/Collection stitching plugin

In reply to this post by Kurt Thorn

I have not used stacks or batches, but when I use filename defined positions for stitching in imageJ or Fiji, y is placed before x. Also it is just one y or x for the number, even if it is multidigit.
Peter
AMT

On Friday, October 18, 2013 6:58 PM, Kurt Thorn <[hidden email]> wrote:

Hi Curtis -

On 10/18/2013 12:16 PM, Curtis Rueden wrote:

>>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>>
>>>
>>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>

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Kurt Thorn

Re: Problem with Grid/Collection stitching plugin

Just to provide an update on this - stitching Micro-Manager images using
the metadata in the OME-TIFF works very well and appears to be quite
robust. I've written up a short description of how to do it:
http://nic.ucsf.edu/dokuwiki/doku.php?id=image_stitching_in_micro-manager
https://micro-manager.org/wiki/Stitching_Micro-Manager_Images

Kurt

On 10/30/2013 2:36 PM, Peter Blankenheim wrote:

> I have not used stacks or batches, but when I use filename defined positions for stitching in imageJ or Fiji, y is placed before x. Also it is just one y or x for the number, even if it is multidigit.
> Peter
> AMT
>
>
>
>
> On Friday, October 18, 2013 6:58 PM, Kurt Thorn <[hidden email]> wrote:
>
> Hi Curtis -
>
> On 10/18/2013 12:16 PM, Curtis Rueden wrote:
>> Hi Kurt,
>>
>>> I'm running grid/collection stitching with the Filename defined
>>> position option, and pointing it to a folder of tif stacks with the
>>> naming convention
>>> tumor_grid_animal04_2_MMStack_1-Pos_{xxx}_{yyy}.ome.tif and the
>>> stitching plugin reports that it opens each stack separately, so I
>>> think that's working OK?
>> What happens if you select "Positions from file" for the Type, and "Defined
>> by image metadata" for the Order?
> This loads and stitches the images properly.
>> I will also reiterate my previous question:
>>> If you run File > Import > Bio-Formats and point it at your
>>> Micro-Manager .txt file, does it properly detect all your stage
>>> positions?
> If I point it to the first ome.tif file, it brings up a dialog asking
> for the positions I want to open. If I point it to the first
> metadata.txt file, I get an error: Unknown file format.
>
> Thanks for your help!
>
> Kurt
>
>> Regards,

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Simon Locke-2

Re: Problem with Grid/Collection stitching plugin

In reply to this post by ctrueden

Hi Curtis,

Just had the opportunity to read your comments to Kurt. From my perspective,
Jerome helped me significantly regarding a very simple solution to my
ultrasound images.

From my reading of all the tasks that people do in multiple areas of science
and medicine, mine is baby steps. However, it has helped a lot.

As a result, I would like to thank you all for your help, comments in
different threads and actually providing ImageJ software.

I will now turn my attention to measuring areas of blood vessels within
tendons.

Thank you very much all of you.

Regards

Dr Simon Locke
MBBS BMed Sci FACSP FFSEM (UK) FRACGP
Sport and Exercise Physician
Bendigo Orthopaedic and Sports Medicine Clinic
176 Barnard st, Bendigo, Victoria, 3550

P:613 5442 5288 F:613 5442 5399 W:sportmovementcentre.com

Centre for Sport+ Movement is now on Facebook
http://www.facebook.com

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis
Rueden
Sent: Thursday, 31 October 2013 5:54 AM
To: [hidden email]
Subject: Re: Problem with Grid/Collection stitching plugin

Hi Kurt,

> I just wanted to thank you with your help with getting this working.

You're very welcome! Glad to hear it is working.

I hope you do not mind me CCing the ImageJ and OME lists. People often ask
for help solving technical problems, but rarely share their success stories
publicly. It helps the morale of the team, as well as future funding, to
know that people find these tools useful.

> I just did some extensive testing and using the image metadata results
> in great stitching of Micro-Manager data. I'm impressed by the
> interoperability of all these different packages, which I guess owes a
> lot to Bioformats and the OME-TIFF file format.

There are many people who deserve thanks:

Stephan Preibisch did the hard work of authoring the stitching plugins.
http://fiji.sc/Stitching#Citation

Melissa Linkert, the primary Bio-Formats developer, implemented the
Micro-Manager reader, which makes extraction of the stage position metadata
possible.
http://openmicroscopy.org/site/about/licensing-attribution/citing-ome

Johannes Schindelin, the maintainer of Fiji, strives daily to ensure that
Fiji's various components remain compatible with one another.
http://fiji.sc/How_to_cite_Fiji%3F

The Micro-Manager team has done outstanding work and been very
collaborative.
http://www.micro-manager.org/wiki/Citing_Micro-Manager

The Open Microscopy Environment team maintains the OME-XML schema, which as
you point out is how the Stitching plugin can read stage position metadata
from so many different formats using Bio-Formats.
http://openmicroscopy.org/site/about/licensing-attribution/citing-ome

Continuing development of these projects would not be possible without the
efforts of the PIs, including Pavel Tomancak, Kevin Eliceiri and Jason
Swedlow. In particular, they organize invaluable "hackathons" where
developers get together to work on such interoperability. IIRC, it was at
one such event where Stephan made the Stitching plugins use Bio-Formats,
with the help of Melissa and myself.

Regards,
Curtis

On Wed, Oct 30, 2013 at 12:42 PM, Kurt Thorn <[hidden email]> wrote:

> Hi Curtis -
>
> I just wanted to thank you with your help with getting this working.
> I just did some extensive testing and using the image metadata results
> in great stitching of Micro-Manager data. I'm impressed by the
> interoperability of all these different packages, which I guess owes a
> lot to Bioformats and the OME-TIFF file format.
>
> Thanks,
> Kurt
>
>
> On 10/18/2013 12:16 PM, Curtis Rueden wrote:
>
>> Hi Kurt,
>>
>> I'm running grid/collection stitching with the Filename defined
>>> position option, and pointing it to a folder of tif stacks with the
>>> naming convention
>>> tumor_grid_animal04_2_MMStack_**1-Pos_{xxx}_{yyy}.ome.tif and the
>>> stitching plugin reports that it opens each stack separately, so I
>>> think that's working OK?
>>>
>> What happens if you select "Positions from file" for the Type, and
>> "Defined by image metadata" for the Order?
>>
>> I will also reiterate my previous question:
>>
>>> If you run File > Import > Bio-Formats and point it at your
>>> Micro-Manager .txt file, does it properly detect all your stage
>>> positions?
>>>
>> Regards,
>> Curtis
>>
>>
>> On Thu, Oct 17, 2013 at 4:01 PM, Kurt Thorn <[hidden email]> wrote:
>>
>> On 10/17/2013 1:41 PM, Curtis Rueden wrote:
>>>
>>> Hi Kurt,
>>>>
>>>> the final stitched image is composed of repeated copies of the
>>>> first
>>>>
>>>>> image stack
>>>>>
>>>>> Grid/Collection stitching uses Bio-Formats to read the stage
>>>>> position
>>>> information as well as the pixels. If you run File > Import >
>>>> Bio-Formats and point it at your Micro-Manager .txt file, does it
>>>> properly detect all your stage positions? Do they open correctly
>>>> individually? If not, this is a Bio-Formats bug rather than a
>>>> problem with the Stitching plugins.
>>>>
>>>> Regards,
>>>> Curtis
>>>>
>>>> I'm running grid/collection stitching with the Filename defined
>>> position
>>> option, and pointing it to a folder of tif stacks with the naming
>>> convention
>>> tumor_grid_animal04_2_MMStack_****1-Pos_{xxx}_{yyy}.ome.tif
>>> and
>>>
>>> the stitching plugin reports that it opens each stack separately, so
>>> I think that's working OK? But perhaps it's a more subtle
>>> interaction between BioFormats and the stitching plugin?
>>>
>>> Thanks,
>>> Kurt
>>>
>>> On Thu, Oct 17, 2013 at 3:31 PM, Kurt Thorn <[hidden email]>
>>>> wrote:
>>>>
>>>> Hi All -
>>>>
>>>>> I'm trying to stitch a set of Z-stacks acquired in Micro-Manager
>>>>> using the Grid/Collection stitching plugin in Fiji. Everything
>>>>> seems to work OK except that the final stitched image is composed
>>>>> of repeated copies of the first image stack in the set rather than
>>>>> stitching the actual stacks at each position. However, the
>>>>> positions of these copies look like they are in the correct place
>>>>> for the locations of the actual tiles. Can anyone provide insight
>>>>> as to what may be going wrong? I've attached the log file and can
>>>>> provide more information as needed.
>>>>>
>>>>> Thanks,
>>>>> Kurt
>>>>>
>>>>> --
>>>>> ImageJ mailing list:
>>>>> http://imagej.nih.gov/ij/list.******html<http://imagej.nih.gov/ij/
>>>>> list.****html>
>>>>> <http://imagej.nih.**gov/ij/list.**html<http://imagej.nih.gov/ij/l
>>>>> ist.**html>
>>>>> >
>>>>>
>>>>> <http://imagej.nih.gov/**ij/**list.html<http://imagej.nih.gov/**ij
>>>>> /list.html>
>>>>> <http://imagej.nih.**gov/ij/list.html<http://imagej.nih.gov/ij/lis
>>>>> t.html>
>>>>> >
>>>>> --
>>>>>
>>>> ImageJ mailing list:
>>>> http://imagej.nih.gov/ij/list.****html<http://imagej.nih.gov/ij/lis
>>>> t.**html>
>>>> <http://imagej.nih.gov/**ij/list.html<http://imagej.nih.gov/ij/list
>>>> .html>
>>>> >
>>>>
>>>>
>>>>
>>>> --
>>> ImageJ mailing list:
>>> http://imagej.nih.gov/ij/list.****html<http://imagej.nih.gov/ij/list
>>> .**html>
>>> <http://imagej.nih.gov/**ij/list.html<http://imagej.nih.gov/ij/list.
>>> html>
>>> >
>>>
>>> --
>> ImageJ mailing list:
>> http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.ht
>> ml>
>>
>>
>>
>
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html