[ome-users] Problem with Grid/Collection stitching plugin

Wed Oct 30 19:54:11 GMT 2013

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 <kurt.thorn at ucsf.edu> 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 <kurt.thorn at ucsf.edu> 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 <kurt.thorn at ucsf.edu>
>>>> 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
>>>>>
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>
>
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