IJ-OpenCV: a plugin connecting ImageJ and OpenCV
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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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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 > . > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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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 > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: IJ-OpenCV: a plugin connecting ImageJ and OpenCV
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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/ -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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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/ > > > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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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/ >> >> >> > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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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/ >>> >>> >>> >> > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: IJ-OpenCV: a plugin connecting ImageJ and OpenCV
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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/ -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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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/ > > > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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