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

Thu Oct 31 23:04:48 GMT 2013

Hi Kurt-

Thanks from all of us at OME for the positive feedback.  Great to hear that things are working.

(And thanks to Curtis for the forward and cross-post-sometimes, it's a good thing!)

Cheers,

Jason

From: ome-users-bounces at lists.openmicroscopy.org.uk [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Curtis Rueden
Sent: Wednesday, October 30, 2013 7:54 PM
To: Kurt Thorn
Cc: ImageJ Interest Group; OME-users mailing list
Subject: Re: [ome-users] 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 <kurt.thorn at ucsf.edu<mailto: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<mailto: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<mailto: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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