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IJ-OpenCV: a plugin connecting ImageJ and OpenCV

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IJ-OpenCV: a plugin connecting ImageJ and OpenCV

joheras
Hi,

I have released a plugin called IJ-OpenCV (
https://github.com/joheras/IJ-OpenCV) that I think that might be useful for
both the ImageJ and OpenCV communities.

This new version of IJ-OpenCV has been built on top of SciJava Common using
SciJava converters.

The main difference of this plugin with the CVForge plugin (
https://github.com/m4dguy/CVForge) is that using IJ-OpenCV regions of
interest detected in OpenCV can be handled using the nice GUI features of
ImageJ.

Several small ImageJ plugins have been developed using the IJ-OpenCV plugin
and can be downloaded from the update site:
http://sites.imagej.net/IJ-OpenCV/ (available in the ImageJ updater). The
biggest development that employ this plugin is the AntibiogramJ tool that
is built on top of ImageJ (https://sourceforge.net/projects/antibiogramj/).

Any feedback will be gladly welcomed.

Best regards,
Jónathan

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Re: IJ-OpenCV: a plugin connecting ImageJ and OpenCV

Jan-2
Since I developed CVForge, I am curious to check out your plugin.
I am rather busy these days, so feedback will come some time later this
week.
You may also contact me on Skype (username: m4dguy).

Cheers,
Jan

On 1/8/2017 5:30 PM, Jónathan Heras wrote:

> Hi,
>
> I have released a plugin called IJ-OpenCV (
> https://github.com/joheras/IJ-OpenCV) that I think that might be useful for
> both the ImageJ and OpenCV communities.
>
> This new version of IJ-OpenCV has been built on top of SciJava Common using
> SciJava converters.
>
> The main difference of this plugin with the CVForge plugin (
> https://github.com/m4dguy/CVForge) is that using IJ-OpenCV regions of
> interest detected in OpenCV can be handled using the nice GUI features of
> ImageJ.
>
> Several small ImageJ plugins have been developed using the IJ-OpenCV plugin
> and can be downloaded from the update site:
> http://sites.imagej.net/IJ-OpenCV/ (available in the ImageJ updater). The
> biggest development that employ this plugin is the AntibiogramJ tool that
> is built on top of ImageJ (https://sourceforge.net/projects/antibiogramj/).
>
> Any feedback will be gladly welcomed.
>
> Best regards,
> Jónathan
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> .
>


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Re: IJ-OpenCV: a plugin connecting ImageJ and OpenCV

ctrueden
In reply to this post by joheras
Hi Jónathan,

Thanks for your work on this bridge! And sorry for the delay in reply.

It is looking really nice! I especially like the YouTube videos linked from
the project page, which demonstrate white hat, black hat, canny edge
detection, convex hull computation, etc. Those are very illustrative and
well executed.

I did file a couple of minor issues in the issue tracker, some of which may
just be me doing things wrong. The main thing I noticed is that it seems
the bridge only works for RGB data right now? It would be nice if either:
A) the bridge could be extended also to support 8-bit, 16-bit, etc.; or B)
the plugins could proactively check for the correct type, and give a normal
ImageJ 1.x style error message when the type is incorrect.

You could also consider creating some content on the ImageJ wiki, maybe at
https://imagej.net/IJ-OpenCV, and https://imagej.net/OpenCV, with the
former briefly introducing the project and linking to your project page on
GitHub, and the latter enumerating the currently available options for
connecting ImageJ to OpenCV.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Sun, Jan 8, 2017 at 10:30 AM, Jónathan Heras <[hidden email]> wrote:

> Hi,
>
> I have released a plugin called IJ-OpenCV (
> https://github.com/joheras/IJ-OpenCV) that I think that might be useful
> for
> both the ImageJ and OpenCV communities.
>
> This new version of IJ-OpenCV has been built on top of SciJava Common using
> SciJava converters.
>
> The main difference of this plugin with the CVForge plugin (
> https://github.com/m4dguy/CVForge) is that using IJ-OpenCV regions of
> interest detected in OpenCV can be handled using the nice GUI features of
> ImageJ.
>
> Several small ImageJ plugins have been developed using the IJ-OpenCV plugin
> and can be downloaded from the update site:
> http://sites.imagej.net/IJ-OpenCV/ (available in the ImageJ updater). The
> biggest development that employ this plugin is the AntibiogramJ tool that
> is built on top of ImageJ (https://sourceforge.net/projects/antibiogramj/
> ).
>
> Any feedback will be gladly welcomed.
>
> Best regards,
> Jónathan
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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Re: IJ-OpenCV: a plugin connecting ImageJ and OpenCV

Burger Wilhelm
Regarding the ImageJ/OpenCV bridge I guess I would prefer a solution on the 'ImageProcessor' level (instead of 'ImagePlus'). I just recalled that I implemented a complete bridge (for all IJ processor types)  a couple of months ago, which I'd be happy to contribute (once I have the time to search for it)...

--Wilhelm


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis Rueden
Sent: Dienstag, 14. März 2017 16:27
To: [hidden email]
Subject: Re: IJ-OpenCV: a plugin connecting ImageJ and OpenCV

Hi Jónathan,

Thanks for your work on this bridge! And sorry for the delay in reply.

It is looking really nice! I especially like the YouTube videos linked from the project page, which demonstrate white hat, black hat, canny edge detection, convex hull computation, etc. Those are very illustrative and well executed.

I did file a couple of minor issues in the issue tracker, some of which may just be me doing things wrong. The main thing I noticed is that it seems the bridge only works for RGB data right now? It would be nice if either:
A) the bridge could be extended also to support 8-bit, 16-bit, etc.; or B) the plugins could proactively check for the correct type, and give a normal ImageJ 1.x style error message when the type is incorrect.

You could also consider creating some content on the ImageJ wiki, maybe at https://imagej.net/IJ-OpenCV, and https://imagej.net/OpenCV, with the former briefly introducing the project and linking to your project page on GitHub, and the latter enumerating the currently available options for connecting ImageJ to OpenCV.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden Did you know ImageJ has a forum? http://forum.imagej.net/



--
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Re: IJ-OpenCV: a plugin connecting ImageJ and OpenCV

joheras
Thanks, implementing the bridge at the ImageProcessor level will be a good
enhancement for the library. Meanwhile, I have modified the plugins to
proactively check for the correct type and give a normal ImageJ error
message when the type is incorrect.

As Curtis suggested, I have created some content on the ImageJ wiki, see
https://imagej.net/IJ-OpenCV, and https://imagej.net/OpenCV.
<https://imagej.net/OpenCV>

Best,
Jónathan

2017-03-15 14:57 GMT+01:00 Burger Wilhelm <[hidden email]>:

> Regarding the ImageJ/OpenCV bridge I guess I would prefer a solution on
> the 'ImageProcessor' level (instead of 'ImagePlus'). I just recalled that I
> implemented a complete bridge (for all IJ processor types)  a couple of
> months ago, which I'd be happy to contribute (once I have the time to
> search for it)...
>
> --Wilhelm
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Curtis Rueden
> Sent: Dienstag, 14. März 2017 16:27
> To: [hidden email]
> Subject: Re: IJ-OpenCV: a plugin connecting ImageJ and OpenCV
>
> Hi Jónathan,
>
> Thanks for your work on this bridge! And sorry for the delay in reply.
>
> It is looking really nice! I especially like the YouTube videos linked
> from the project page, which demonstrate white hat, black hat, canny edge
> detection, convex hull computation, etc. Those are very illustrative and
> well executed.
>
> I did file a couple of minor issues in the issue tracker, some of which
> may just be me doing things wrong. The main thing I noticed is that it
> seems the bridge only works for RGB data right now? It would be nice if
> either:
> A) the bridge could be extended also to support 8-bit, 16-bit, etc.; or B)
> the plugins could proactively check for the correct type, and give a normal
> ImageJ 1.x style error message when the type is incorrect.
>
> You could also consider creating some content on the ImageJ wiki, maybe at
> https://imagej.net/IJ-OpenCV, and https://imagej.net/OpenCV, with the
> former briefly introducing the project and linking to your project page on
> GitHub, and the latter enumerating the currently available options for
> connecting ImageJ to OpenCV.
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden Did you
> know ImageJ has a forum? http://forum.imagej.net/
>
>
>

--
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Re: IJ-OpenCV: a plugin connecting ImageJ and OpenCV

ctrueden
Hi Jónathan,

> I have modified the plugins to proactively check for the correct type
> and give a normal ImageJ error message when the type is incorrect.
>
> As Curtis suggested, I have created some content on the ImageJ wiki,
> see https://imagej.net/IJ-OpenCV, and https://imagej.net/OpenCV.

Awesome, it is great to see your energy and effort improving this useful
tool. As long as you keep the project actively maintained, I think it will
be very useful to lots of people—already it has come up on the ImageJ
Gitter channel [1]. :-)

Regards,
Curtis

[1] https://gitter.im/imagej/imagej/archives/2017/03/15

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Wed, Mar 15, 2017 at 1:02 PM, Jónathan Heras <[hidden email]> wrote:

> Thanks, implementing the bridge at the ImageProcessor level will be a good
> enhancement for the library. Meanwhile, I have modified the plugins to
> proactively check for the correct type and give a normal ImageJ error
> message when the type is incorrect.
>
> As Curtis suggested, I have created some content on the ImageJ wiki, see
> https://imagej.net/IJ-OpenCV, and https://imagej.net/OpenCV.
> <https://imagej.net/OpenCV>
>
> Best,
> Jónathan
>
> 2017-03-15 14:57 GMT+01:00 Burger Wilhelm <[hidden email]>
> :
>
>> Regarding the ImageJ/OpenCV bridge I guess I would prefer a solution on
>> the 'ImageProcessor' level (instead of 'ImagePlus'). I just recalled that I
>> implemented a complete bridge (for all IJ processor types)  a couple of
>> months ago, which I'd be happy to contribute (once I have the time to
>> search for it)...
>>
>> --Wilhelm
>>
>>
>> -----Original Message-----
>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>> Curtis Rueden
>> Sent: Dienstag, 14. März 2017 16:27
>> To: [hidden email]
>> Subject: Re: IJ-OpenCV: a plugin connecting ImageJ and OpenCV
>>
>> Hi Jónathan,
>>
>> Thanks for your work on this bridge! And sorry for the delay in reply.
>>
>> It is looking really nice! I especially like the YouTube videos linked
>> from the project page, which demonstrate white hat, black hat, canny edge
>> detection, convex hull computation, etc. Those are very illustrative and
>> well executed.
>>
>> I did file a couple of minor issues in the issue tracker, some of which
>> may just be me doing things wrong. The main thing I noticed is that it
>> seems the bridge only works for RGB data right now? It would be nice if
>> either:
>> A) the bridge could be extended also to support 8-bit, 16-bit, etc.; or
>> B) the plugins could proactively check for the correct type, and give a
>> normal ImageJ 1.x style error message when the type is incorrect.
>>
>> You could also consider creating some content on the ImageJ wiki, maybe
>> at https://imagej.net/IJ-OpenCV, and https://imagej.net/OpenCV, with the
>> former briefly introducing the project and linking to your project page on
>> GitHub, and the latter enumerating the currently available options for
>> connecting ImageJ to OpenCV.
>>
>> Regards,
>> Curtis
>>
>> --
>> Curtis Rueden
>> LOCI software architect - https://loci.wisc.edu/software
>> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden Did you
>> know ImageJ has a forum? http://forum.imagej.net/
>>
>>
>>
>

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Re: IJ-OpenCV: a plugin connecting ImageJ and OpenCV

joheras
That is great! I will try to mantain the project active and keep improving
it.
Best,
Jónathan

2017-03-15 19:40 GMT+01:00 Curtis Rueden <[hidden email]>:

> Hi Jónathan,
>
> > I have modified the plugins to proactively check for the correct type
> > and give a normal ImageJ error message when the type is incorrect.
> >
> > As Curtis suggested, I have created some content on the ImageJ wiki,
> > see https://imagej.net/IJ-OpenCV, and https://imagej.net/OpenCV.
>
> Awesome, it is great to see your energy and effort improving this useful
> tool. As long as you keep the project actively maintained, I think it will
> be very useful to lots of people—already it has come up on the ImageJ
> Gitter channel [1]. :-)
>
> Regards,
> Curtis
>
> [1] https://gitter.im/imagej/imagej/archives/2017/03/15
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Wed, Mar 15, 2017 at 1:02 PM, Jónathan Heras <[hidden email]> wrote:
>
>> Thanks, implementing the bridge at the ImageProcessor level will be a
>> good enhancement for the library. Meanwhile, I have modified the plugins to
>> proactively check for the correct type and give a normal ImageJ error
>> message when the type is incorrect.
>>
>> As Curtis suggested, I have created some content on the ImageJ wiki, see
>> https://imagej.net/IJ-OpenCV, and https://imagej.net/OpenCV.
>> <https://imagej.net/OpenCV>
>>
>> Best,
>> Jónathan
>>
>> 2017-03-15 14:57 GMT+01:00 Burger Wilhelm <[hidden email]
>> >:
>>
>>> Regarding the ImageJ/OpenCV bridge I guess I would prefer a solution on
>>> the 'ImageProcessor' level (instead of 'ImagePlus'). I just recalled that I
>>> implemented a complete bridge (for all IJ processor types)  a couple of
>>> months ago, which I'd be happy to contribute (once I have the time to
>>> search for it)...
>>>
>>> --Wilhelm
>>>
>>>
>>> -----Original Message-----
>>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>>> Curtis Rueden
>>> Sent: Dienstag, 14. März 2017 16:27
>>> To: [hidden email]
>>> Subject: Re: IJ-OpenCV: a plugin connecting ImageJ and OpenCV
>>>
>>> Hi Jónathan,
>>>
>>> Thanks for your work on this bridge! And sorry for the delay in reply.
>>>
>>> It is looking really nice! I especially like the YouTube videos linked
>>> from the project page, which demonstrate white hat, black hat, canny edge
>>> detection, convex hull computation, etc. Those are very illustrative and
>>> well executed.
>>>
>>> I did file a couple of minor issues in the issue tracker, some of which
>>> may just be me doing things wrong. The main thing I noticed is that it
>>> seems the bridge only works for RGB data right now? It would be nice if
>>> either:
>>> A) the bridge could be extended also to support 8-bit, 16-bit, etc.; or
>>> B) the plugins could proactively check for the correct type, and give a
>>> normal ImageJ 1.x style error message when the type is incorrect.
>>>
>>> You could also consider creating some content on the ImageJ wiki, maybe
>>> at https://imagej.net/IJ-OpenCV, and https://imagej.net/OpenCV, with
>>> the former briefly introducing the project and linking to your project page
>>> on GitHub, and the latter enumerating the currently available options for
>>> connecting ImageJ to OpenCV.
>>>
>>> Regards,
>>> Curtis
>>>
>>> --
>>> Curtis Rueden
>>> LOCI software architect - https://loci.wisc.edu/software
>>> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden Did you
>>> know ImageJ has a forum? http://forum.imagej.net/
>>>
>>>
>>>
>>
>

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Re: IJ-OpenCV: a plugin connecting ImageJ and OpenCV

Burger Wilhelm
In reply to this post by joheras
Hi Jonathan,

I found my earlier implementation of the OpenCV/ImageJ bridge (which I had originally built to work with the opencv.org wrapper) and adapted it to the ‘bytedeco.javacv’ API that IJ-OpenCV uses. It operates on the image processor level and an initial version can be seen here:

https://github.com/imagingbook/IJ-OpenCV-WB/blob/master/src/main/java/imagingbook/opencv/Convert.java

A modified example IJ plugin can be found here:

https://github.com/imagingbook/IJ-OpenCV-WB/blob/master/src/main/java/opencv_examples/Adaptive_ThresholdJ.java

I know that there are more ‘modern’ ways to design such things but I like to keep the code simple, readable by non-experts, and with minimal dependencies (much in the spirit of IJ1).

--Wilhelm


From: Jónathan Heras [mailto:[hidden email]]
Sent: Mittwoch, 15. März 2017 19:03
To: Burger Wilhelm <[hidden email]>
Cc: [hidden email]; Curtis Rueden <[hidden email]>
Subject: Re: IJ-OpenCV: a plugin connecting ImageJ and OpenCV

Thanks, implementing the bridge at the ImageProcessor level will be a good enhancement for the library. Meanwhile, I have modified the plugins to proactively check for the correct type and give a normal ImageJ error message when the type is incorrect.
As Curtis suggested, I have created some content on the ImageJ wiki, see https://imagej.net/IJ-OpenCV, and https://imagej.net/OpenCV.<https://imagej.net/OpenCV>
Best,
Jónathan

2017-03-15 14:57 GMT+01:00 Burger Wilhelm <[hidden email]<mailto:[hidden email]>>:
Regarding the ImageJ/OpenCV bridge I guess I would prefer a solution on the 'ImageProcessor' level (instead of 'ImagePlus'). I just recalled that I implemented a complete bridge (for all IJ processor types)  a couple of months ago, which I'd be happy to contribute (once I have the time to search for it)...

--Wilhelm


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]<mailto:[hidden email]>] On Behalf Of Curtis Rueden
Sent: Dienstag, 14. März 2017 16:27
To: [hidden email]<mailto:[hidden email]>
Subject: Re: IJ-OpenCV: a plugin connecting ImageJ and OpenCV

Hi Jónathan,

Thanks for your work on this bridge! And sorry for the delay in reply.

It is looking really nice! I especially like the YouTube videos linked from the project page, which demonstrate white hat, black hat, canny edge detection, convex hull computation, etc. Those are very illustrative and well executed.

I did file a couple of minor issues in the issue tracker, some of which may just be me doing things wrong. The main thing I noticed is that it seems the bridge only works for RGB data right now? It would be nice if either:
A) the bridge could be extended also to support 8-bit, 16-bit, etc.; or B) the plugins could proactively check for the correct type, and give a normal ImageJ 1.x style error message when the type is incorrect.

You could also consider creating some content on the ImageJ wiki, maybe at https://imagej.net/IJ-OpenCV, and https://imagej.net/OpenCV, with the former briefly introducing the project and linking to your project page on GitHub, and the latter enumerating the currently available options for connecting ImageJ to OpenCV.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden Did you know ImageJ has a forum? http://forum.imagej.net/



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Re: IJ-OpenCV: a plugin connecting ImageJ and OpenCV

joheras
That is great. Do you mind if I include it in IJ-OpenCV?
I would like to also adapt the rest of plugins that are provided as
examples in IJ-OpenCV to use these converters.
Best,
Jónathan

2017-03-22 10:14 GMT+01:00 Burger Wilhelm <[hidden email]>:

> Hi Jonathan,
>
>
>
> I found my earlier implementation of the OpenCV/ImageJ bridge (which I had
> originally built to work with the opencv.org wrapper) and adapted it to
> the ‘bytedeco.javacv’ API that IJ-OpenCV uses. It operates on the image
> processor level and an initial version can be seen here:
>
>
>
> https://github.com/imagingbook/IJ-OpenCV-WB/blob/master/src/main/java/
> imagingbook/opencv/Convert.java
>
>
>
> A modified example IJ plugin can be found here:
>
>
>
> https://github.com/imagingbook/IJ-OpenCV-WB/blob/
> master/src/main/java/opencv_examples/Adaptive_ThresholdJ.java
>
>
>
> I know that there are more ‘modern’ ways to design such things but I like
> to keep the code simple, readable by non-experts, and with minimal
> dependencies (much in the spirit of IJ1).
>
>
>
> --Wilhelm
>
>
>
>
>
> *From:* Jónathan Heras [mailto:[hidden email]]
> *Sent:* Mittwoch, 15. März 2017 19:03
> *To:* Burger Wilhelm <[hidden email]>
> *Cc:* [hidden email]; Curtis Rueden <[hidden email]>
> *Subject:* Re: IJ-OpenCV: a plugin connecting ImageJ and OpenCV
>
>
>
> Thanks, implementing the bridge at the ImageProcessor level will be a good
> enhancement for the library. Meanwhile, I have modified the plugins to
> proactively check for the correct type and give a normal ImageJ error
> message when the type is incorrect.
>
> As Curtis suggested, I have created some content on the ImageJ wiki, see
> https://imagej.net/IJ-OpenCV, and https://imagej.net/OpenCV.
> <https://imagej.net/OpenCV>
>
> Best,
>
> Jónathan
>
>
>
> 2017-03-15 14:57 GMT+01:00 Burger Wilhelm <[hidden email]
> >:
>
> Regarding the ImageJ/OpenCV bridge I guess I would prefer a solution on
> the 'ImageProcessor' level (instead of 'ImagePlus'). I just recalled that I
> implemented a complete bridge (for all IJ processor types)  a couple of
> months ago, which I'd be happy to contribute (once I have the time to
> search for it)...
>
> --Wilhelm
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Curtis Rueden
> Sent: Dienstag, 14. März 2017 16:27
> To: [hidden email]
> Subject: Re: IJ-OpenCV: a plugin connecting ImageJ and OpenCV
>
> Hi Jónathan,
>
> Thanks for your work on this bridge! And sorry for the delay in reply.
>
> It is looking really nice! I especially like the YouTube videos linked
> from the project page, which demonstrate white hat, black hat, canny edge
> detection, convex hull computation, etc. Those are very illustrative and
> well executed.
>
> I did file a couple of minor issues in the issue tracker, some of which
> may just be me doing things wrong. The main thing I noticed is that it
> seems the bridge only works for RGB data right now? It would be nice if
> either:
> A) the bridge could be extended also to support 8-bit, 16-bit, etc.; or B)
> the plugins could proactively check for the correct type, and give a normal
> ImageJ 1.x style error message when the type is incorrect.
>
> You could also consider creating some content on the ImageJ wiki, maybe at
> https://imagej.net/IJ-OpenCV, and https://imagej.net/OpenCV, with the
> former briefly introducing the project and linking to your project page on
> GitHub, and the latter enumerating the currently available options for
> connecting ImageJ to OpenCV.
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden Did you
> know ImageJ has a forum? http://forum.imagej.net/
>
>
>

--
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