Stitching 1.1 Release

[Mark Hiner-2]

Dear Stitching users,

 You may have noticed that the Stitching plugins (Plugins > Stitching >
Pairwise stitching, and Plugins > Stitching > Grid/Collection stitching)
take a fairly significant amount of time to get through the fusion process.
Today, I am pleased to announce Stitching version 1.1 which features
greatly reduced fusion times, available now in Fiji (just run Help > Update
Fiji).

 Briefly, the old fusion paradigm was to iterate through output image's
pixels and, at each position, check every input image to see if they
overlapped at that position. By pre-computing these contribution ranges at
the start of fusion, we can see significant performance improvements.

 The actual speedup will depend on the number of images being stitched and
how much they overlap, but on a test dataset with ~150 images and 10%
overlap, the new fusion method was over an order of magnitude faster (80
seconds + ~10 seconds of pre-computation, down from 20 minutes with the
previous Stitching version).

 We have done a number of tests comparing the output of the new plugin with
the previous Stitching version, and as far as we can tell the new results
are pixel-perfect matches with the old, so the quality of your data should
not be affected.

  If you do run into any problems, errors, mis-stitches, etc... or have any
questions/comments about the Stitching plugin and its uses, please let us
know!

Happy stitching!
- Mark

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[chin]

Hi MArk,

Is this update only available in Fiji or also available in the standalone
package downloaded for Imagej?

Best,

chin





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[Mark Hiner-2]

Hi Chin,

 Fiji <http://fiji.sc/Fiji> is definitely the recommended way to get the
Stitching update, as it allows you to easily stay current with the latest
plugin versions (and includes a number of other useful plugins/features).

 But, you can always download the most recent Stitching build from the
LOCI/ImageJ
Jenkins<http://jenkins.imagej.net/job/Stitching/lastSuccessfulBuild/artifact/target/Stitching_-2.0.0-SNAPSHOT.jar>
.

 Additionally, the source is freely available on
GitHub<https://github.com/fiji/Stitching>
.

 It is important to understand that as development continues on the
Stitching plugin, the versions obtained from Jenkins or GitHub may differ
from what's uploaded to Fiji. The Fiji version will always be what we
recommend for users.

Thanks for the question, and let me know if there's any other help I can
provide.

Regards,
Mark


On Sun, May 11, 2014 at 8:31 PM, chin <[hidden email]> wrote:

> Hi MArk,
>
> Is this update only available in Fiji or also available in the standalone
> package downloaded for Imagej?
>
> Best,
>
> chin
>
>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Stitching-1-1-Release-tp5007668p5007685.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[chin]

Hi Mark,

Thanks for the explanation.

My collegues and me always use "old" stitching plugin in Imagej. We will try
to use Fiji on stitching
images.

Best,

chin



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[Mark Hiner-2]

Hi Chin,

 That's great! Just let me know if you have any difficulties.

Thanks,
Mark


On Mon, May 12, 2014 at 8:56 AM, chin <[hidden email]> wrote:

> Hi Mark,
>
> Thanks for the explanation.
>
> My collegues and me always use "old" stitching plugin in Imagej. We will
> try
> to use Fiji on stitching
> images.
>
> Best,
>
> chin
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Stitching-1-1-Release-tp5007668p5007698.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Peter Haub]

Hi Mark,
Dear list,

version 1.1 of the Stitching plugin is currently included in FIJI.
The source code on github is version 1.11.

Is there a development schedule for this plugin?
Is there a plan to release version 1.11?
Where can the source code of 1.1 be found?

Thanks for any answer.
Regards,
Peter

On 09.05.2014 18:40, Mark Hiner wrote:

> Dear Stitching users,
>
>   You may have noticed that the Stitching plugins (Plugins > Stitching >
> Pairwise stitching, and Plugins > Stitching > Grid/Collection stitching)
> take a fairly significant amount of time to get through the fusion process.
> Today, I am pleased to announce Stitching version 1.1 which features
> greatly reduced fusion times, available now in Fiji (just run Help > Update
> Fiji).
>
>   Briefly, the old fusion paradigm was to iterate through output image's
> pixels and, at each position, check every input image to see if they
> overlapped at that position. By pre-computing these contribution ranges at
> the start of fusion, we can see significant performance improvements.
>
>   The actual speedup will depend on the number of images being stitched and
> how much they overlap, but on a test dataset with ~150 images and 10%
> overlap, the new fusion method was over an order of magnitude faster (80
> seconds + ~10 seconds of pre-computation, down from 20 minutes with the
> previous Stitching version).
>
>   We have done a number of tests comparing the output of the new plugin with
> the previous Stitching version, and as far as we can tell the new results
> are pixel-perfect matches with the old, so the quality of your data should
> not be affected.
>
>    If you do run into any problems, errors, mis-stitches, etc... or have any
> questions/comments about the Stitching plugin and its uses, please let us
> know!
>
> Happy stitching!
> - Mark
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[ctrueden]

Hi Peter,

> Is there a plan to release version 1.11?

A new version of the Stitching plugin will be uploaded tomorrow as part of
the "Big Upload"; see:

https://list.nih.gov/cgi-bin/wa.exe?A2=IMAGEJ;a9147af3.1412

> Is there a development schedule for this plugin?

There is no formal roadmap, though there is typically a rapid turnaround on
releases after bugs are fixed.

> Where can the source code of 1.1 be found?

It is in the Git history, of course. Unfortunately, the version embedded in
the source code has diverged from the version embedded in the Maven POM. We
will need to reconcile this.

For now, the way to find the right source is:
- Unpack the JAR file in question.
- Look at the Implementation-Build entry in META-INF/MANIFEST.MF.

In the case of the Stitching plugin currently shipped with Fiji, the
revision is:
e6f18ad79afdd542db8030291a1dfc73e6ba130e

So the source is at:
https://github.com/fiji/Stitching/commit/e6f18ad79afdd542db8030291a1dfc73e6ba130e

Regards,
Curtis

On Thu, Dec 18, 2014 at 11:25 AM, Peter Haub <[hidden email]> wrote:

>
> Hi Mark,
> Dear list,
>
> version 1.1 of the Stitching plugin is currently included in FIJI.
> The source code on github is version 1.11.
>
> Is there a development schedule for this plugin?
> Is there a plan to release version 1.11?
> Where can the source code of 1.1 be found?
>
> Thanks for any answer.
> Regards,
> Peter
>
>
> On 09.05.2014 18:40, Mark Hiner wrote:
>
>> Dear Stitching users,
>>
>>   You may have noticed that the Stitching plugins (Plugins > Stitching >
>> Pairwise stitching, and Plugins > Stitching > Grid/Collection stitching)
>> take a fairly significant amount of time to get through the fusion
>> process.
>> Today, I am pleased to announce Stitching version 1.1 which features
>> greatly reduced fusion times, available now in Fiji (just run Help >
>> Update
>> Fiji).
>>
>>   Briefly, the old fusion paradigm was to iterate through output image's
>> pixels and, at each position, check every input image to see if they
>> overlapped at that position. By pre-computing these contribution ranges at
>> the start of fusion, we can see significant performance improvements.
>>
>>   The actual speedup will depend on the number of images being stitched
>> and
>> how much they overlap, but on a test dataset with ~150 images and 10%
>> overlap, the new fusion method was over an order of magnitude faster (80
>> seconds + ~10 seconds of pre-computation, down from 20 minutes with the
>> previous Stitching version).
>>
>>   We have done a number of tests comparing the output of the new plugin
>> with
>> the previous Stitching version, and as far as we can tell the new results
>> are pixel-perfect matches with the old, so the quality of your data should
>> not be affected.
>>
>>    If you do run into any problems, errors, mis-stitches, etc... or have
>> any
>> questions/comments about the Stitching plugin and its uses, please let us
>> know!
>>
>> Happy stitching!
>> - Mark
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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