looking for a simple Maven project implementing an ImageJ 2.x plugin
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in the past I used the Process_Pixels Maven example as a starting point to make plugins using Maven.
Now I like to switch to IJ2, I’m wondering whether there is an IJ2 example project available. Or can I easily convert Process_Pixels to IJ2? thanks, Gerrit. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: looking for a simple Maven project implementing an ImageJ 2.x plugin
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Hi Gerrit,
>Now I like to switch to IJ2, I’m wondering whether there is an IJ2 example project available. The ImageJ-tutorials <https://github.com/imagej/imagej-tutorials> project is the intended starting point for developers. There is also an accompanying entry <http://imagej.net/Writing_ImageJ2_plugins> in the Development <http://imagej.net/Development> section of the ImageJ wiki. Thanks for the interest in ImageJ2 - let us know if you have any questions or run into problems! Best, Mark On Fri, Dec 19, 2014 at 4:30 AM, Polder, Gerrit <[hidden email]> wrote: > > in the past I used the Process_Pixels Maven example as a starting point to > make plugins using Maven. > Now I like to switch to IJ2, I’m wondering whether there is an IJ2 example > project available. > Or can I easily convert Process_Pixels to IJ2? > > thanks, > Gerrit. > > -- > 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 gerrit
thanks Mark, this is exactly where I was looking for.
Gerrit. On 20 dec. 2014, at 06:00, IMAGEJ automatic digest system <[hidden email]<mailto:[hidden email]>> wrote: Hi Gerrit, Now I like to switch to IJ2, I’m wondering whether there is an IJ2 example project available. The ImageJ-tutorials <https://github.com/imagej/imagej-tutorials> project is the intended starting point for developers. There is also an accompanying entry <http://imagej.net/Writing_ImageJ2_plugins> in the Development <http://imagej.net/Development> section of the ImageJ wiki. Thanks for the interest in ImageJ2 - let us know if you have any questions or run into problems! Best, Mark -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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I succeeded in making a maven project, but I’m still struggling in finding demo code and the api for writing a simple plugin.
For instance how to code a pluginfiler in imagej2? public class Get_blue_region implements PlugInFilter { ImagePlus imp; boolean DEBUG = false; public int setup(String arg, ImagePlus imp) { this.imp = imp; if (arg.equals("about")) { showAbout(); return DONE; } return DOES_RGB; } public void run(ImageProcessor ip) { ImagePlus calim = new ImagePlus("Blue Part", ip); ……………. } } sorry if this is a silly question, but I got stuck in all wikis and github repositories. Gerrit. On 20 Dec 2014, at 19:11, Polder, Gerrit <[hidden email]<mailto:[hidden email]>> wrote: thanks Mark, this is exactly where I was looking for. Gerrit. On 20 dec. 2014, at 06:00, IMAGEJ automatic digest system <[hidden email]<mailto:[hidden email]>> wrote: Hi Gerrit, Now I like to switch to IJ2, I’m wondering whether there is an IJ2 example project available. The ImageJ-tutorials <https://github.com/imagej/imagej-tutorials> project is the intended starting point for developers. There is also an accompanying entry <http://imagej.net/Writing_ImageJ2_plugins> in the Development <http://imagej.net/Development> section of the ImageJ wiki. Thanks for the interest in ImageJ2 - let us know if you have any questions or run into problems! Best, Mark -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Gerrit,
did you have a look at the fabulous tutorial written by Werner Bailer? <http://imagingbook.com/imagej-tutorial/> "Download Tutorial (pdf)" Most of what you need can be found in this text and the accompanying examples. HTH Herbie :::::::::::::::::::::::::::::::::::::::: On 07.01.15 16:40, Polder, Gerrit wrote: > I succeeded in making a maven project, but I’m still struggling in > finding demo code and the api for writing a simple plugin. For > instance how to code a pluginfiler in imagej2? > > public class Get_blue_region implements PlugInFilter { ImagePlus > imp; boolean DEBUG = false; > > public int setup(String arg, ImagePlus imp) { this.imp = imp; if > (arg.equals("about")) { showAbout(); return DONE; } return DOES_RGB; > } > > public void run(ImageProcessor ip) { ImagePlus calim = new > ImagePlus("Blue Part", ip); ……………. } } > > sorry if this is a silly question, but I got stuck in all wikis and > github repositories. > > Gerrit. > > > On 20 Dec 2014, at 19:11, Polder, Gerrit > <[hidden email]<mailto:[hidden email]>> wrote: > > thanks Mark, this is exactly where I was looking for. > > Gerrit. > > On 20 dec. 2014, at 06:00, IMAGEJ automatic digest system > <[hidden email]<mailto:[hidden email]>> wrote: > > Hi Gerrit, > > Now I like to switch to IJ2, I’m wondering whether there is an IJ2 > example project available. > > The ImageJ-tutorials <https://github.com/imagej/imagej-tutorials> > project is the intended starting point for developers. There is also > an accompanying entry <http://imagej.net/Writing_ImageJ2_plugins> in > the Development <http://imagej.net/Development> section of the ImageJ > wiki. > > Thanks for the interest in ImageJ2 - let us know if you have any > questions or run into problems! > > Best, 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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In reply to this post by gerrit
Dear Wayne,
thanks for the prompt reply, my question was indeed not clear stated. Yes this is a ImageJ1 plugin, but since I need to add some functionality to it I thought it would be worthwhile to convert it to the current ImageJ platform, in order to make it future proof. As ImageJ2 now is the production release I decided to give it a try. Is it true that questions related to the development of user plugins should be addressed to imagej-devel? I’m also curious about other plugin developers, how many still develop in ImageJ1, and how many switched already to ImageJ2? By the way I already found part of the problem. The Image I tested my plugin tryout on was an old ImageJ image, instead of a new dataset ‘image’. After enabling the SCIFIO library I could input an image in my plugin. But still I think need more documentation and examples, kind of ‘guide for switchers’. best regards, Gerrit. On 7 jan. 2015, at 17:26, Rasband, Wayne (NIH/NIMH) [E] <[hidden email]<mailto:[hidden email]>> wrote: Dear Polder, Your plugin is not an ImageJ2 plugin. It is an ImageJ plugin that you can easily compile and run it using the Plugins>Compile and Run command. Questions about ImageJ2 and mavin should be sent to the image-dev mailing list. http://imagej.net/mailman/listinfo/imagej-devel Best regards, -wayne On Jan 7, 2015, at 10:40 AM, Polder, Gerrit <[hidden email]<mailto:[hidden email]>> wrote: I succeeded in making a maven project, but I’m still struggling in finding demo code and the api for writing a simple plugin. For instance how to code a pluginfiler in imagej2? public class Get_blue_region implements PlugInFilter { ImagePlus imp; boolean DEBUG = false; public int setup(String arg, ImagePlus imp) { this.imp = imp; if (arg.equals("about")) { showAbout(); return DONE; } return DOES_RGB; } public void run(ImageProcessor ip) { ImagePlus calim = new ImagePlus("Blue Part", ip); ……………. } } sorry if this is a silly question, but I got stuck in all wikis and github repositories. Gerrit. On 20 Dec 2014, at 19:11, Polder, Gerrit <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>> wrote: thanks Mark, this is exactly where I was looking for. Gerrit. On 20 dec. 2014, at 06:00, IMAGEJ automatic digest system <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>> wrote: Hi Gerrit, Now I like to switch to IJ2, I’m wondering whether there is an IJ2 example project available. The ImageJ-tutorials <https://github.com/imagej/imagej-tutorials> project is the intended starting point for developers. There is also an accompanying entry <http://imagej.net/Writing_ImageJ2_plugins> in the Development <http://imagej.net/Development> section of the ImageJ wiki. Thanks for the interest in ImageJ2 - let us know if you have any questions or run into problems! Best, 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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In reply to this post by gerrit
Herbie,
thanks, yes I know that one, helped me a lot in the past, but now I am looking for a similar one covering ImageJ2. Gerrit On 8 Jan 2015, at 06:00, IMAGEJ automatic digest system <[hidden email]<mailto:[hidden email]>> wrote: Date: Wed, 7 Jan 2015 17:01:52 +0100 From: Herbie <[hidden email]<mailto:[hidden email]>> Subject: Re: looking for a simple Maven project implementing an ImageJ 2.x plugin Gerrit, did you have a look at the fabulous tutorial written by Werner Bailer? <http://imagingbook.com/imagej-tutorial/> "Download Tutorial (pdf)" Most of what you need can be found in this text and the accompanying examples. HTH Herbie -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Gerrit
As others have mentioned this question may be more appropriate for the dev list. I've gotten a lot of useful advice there. That being said you might want to look at this example. It shows how to write a command, in imagej2 a command is a type of plugin. https://github.com/imagej/imagej-tutorials/blob/master/simple-commands/src/main/java/GradientImage.java This shows how to get a dataset into your plugin... after that you will want to learn how to manipulate images. ImageJ2 plugins often use imglib2 for low level algorithms. So checking out the imglib2 tutorials would be helpful. http://fiji.sc/ImgLib2_Examples One tip that might be helpful. You will want to get comfortable getting the image data from the dataset. You will need something like data.getImgPlus().getImg(). Also you might want to learn about imagej-ops. https://github.com/imagej/imagej-ops Brian On Thu, Jan 8, 2015 at 7:35 AM, Polder, Gerrit <[hidden email]> wrote: > Herbie, > > thanks, yes I know that one, helped me a lot in the past, but now I am > looking for a similar one covering ImageJ2. > > Gerrit > > On 8 Jan 2015, at 06:00, IMAGEJ automatic digest system < > [hidden email]<mailto:[hidden email]>> wrote: > > Date: Wed, 7 Jan 2015 17:01:52 +0100 > From: Herbie <[hidden email]<mailto:[hidden email]>> > Subject: Re: looking for a simple Maven project implementing an ImageJ 2.x > plugin > > Gerrit, > > did you have a look at the fabulous tutorial written by Werner Bailer? > > <http://imagingbook.com/imagej-tutorial/> > > "Download Tutorial (pdf)" > > Most of what you need can be found in this text and the accompanying > examples. > > HTH > > Herbie > > -- > 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 gerrit
Dear Wayne,
I’m a little bit confused reading ImageJ2 is still in beta. Im not a fulltime ImageJ user, but once and a while customers ask me to develop imaging software in ImageJ. Mainly I'm using Matlab and Halcon. I’m spending about 4-8 weeks a year on ImageJ. My previous project was about a year ago. Currently I need to update some features on one of my plugins, so given the fact that ImageJ2 reached the 2.0.0 stage in june last year, and also since it is the default ImageJ version in Fiji, as I already said I thought it would be worthwhile to convert it to the current ImageJ platform, in order to make it future proof. So from your message I conclude that although my customer uses Fiji, I better stick to ImageJ1, in order not to provide him with a buggy plugin. On the last two conferences I’v seen a lot of nice ImageJ2 and ImgLib features, and promises about availability. Is there information available about ImageJ’s roadmap? As you suggested I will send this message also to Imagej-devel, sorry for cross-posting. best regards, Gerrit. On 8 Jan 2015, at 05:50, Rasband, Wayne (NIH/NIMH) [E] <[hidden email]> wrote: > Dear Gerrit, > >> On Jan 7, 2015, at 2:54 PM, Polder, Gerrit <[hidden email]> wrote: >> >> Dear Wayne, >> >> thanks for the prompt reply, my question was indeed not clear stated. >> Yes this is a ImageJ1 plugin, but since I need to add some functionality to it I thought it would be worthwhile to convert it to the current ImageJ platform, in order to make it future proof. >> As ImageJ2 now is the production release I decided to give it a try. > > ImageJ2 is not the production release. It is beta software. The two options in Fiji’s Edit>Option>ImageJ2 dialog (ImageJ2 data structures and SCIFIO) are disabled by default because they are buggy. > >> Is it true that questions related to the development of user plugins should be addressed to imagej-devel? > > Question related to development of ImageJ2 plugins, imglib2 and SCIFIO should be addressed to imagej-devel. > >> I’m also curious about other plugin developers, how many still develop in ImageJ1, and how many switched already to ImageJ2? > > Most developers are still writing ImageJ plugins. > >> By the way I already found part of the problem. The Image I tested my plugin tryout on was an old ImageJ image, instead of a new dataset ‘image’. After enabling the SCIFIO library I could input an image in my plugin. >> But still I think need more documentation and examples, kind of ‘guide for switchers’. > > You should bring these issues up on the imagej-devel mailing list. > > Best regards, > > -wayne > > >> On 7 jan. 2015, at 17:26, Rasband, Wayne (NIH/NIMH) [E] <[hidden email]<mailto:[hidden email]>> wrote: >> >> Dear Polder, >> >> Your plugin is not an ImageJ2 plugin. It is an ImageJ plugin that you can easily compile and run it using the Plugins>Compile and Run command. Questions about ImageJ2 and mavin should be sent to the image-dev mailing list. >> >> http://imagej.net/mailman/listinfo/imagej-devel >> >> Best regards, >> >> -wayne >> >> >> >> On Jan 7, 2015, at 10:40 AM, Polder, Gerrit <[hidden email]<mailto:[hidden email]>> wrote: >> >> I succeeded in making a maven project, but I’m still struggling in finding demo code and the api for writing a simple plugin. >> For instance how to code a pluginfiler in imagej2? >> >> public class Get_blue_region implements PlugInFilter { >> ImagePlus imp; >> boolean DEBUG = false; >> >> public int setup(String arg, ImagePlus imp) { >> this.imp = imp; >> if (arg.equals("about")) { >> showAbout(); >> return DONE; >> } >> return DOES_RGB; >> } >> >> public void run(ImageProcessor ip) { >> ImagePlus calim = new ImagePlus("Blue Part", ip); >> ……………. >> } >> } >> >> sorry if this is a silly question, but I got stuck in all wikis and github repositories. >> >> Gerrit. >> >> >> On 20 Dec 2014, at 19:11, Polder, Gerrit <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>> wrote: >> >> thanks Mark, this is exactly where I was looking for. >> >> Gerrit. >> >> On 20 dec. 2014, at 06:00, IMAGEJ automatic digest system <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>> wrote: >> >> Hi Gerrit, >> >> Now I like to switch to IJ2, I’m wondering whether there is an IJ2 example >> project available. >> >> The ImageJ-tutorials <https://github.com/imagej/imagej-tutorials> project >> is the intended starting point for developers. There is also an accompanying >> entry <http://imagej.net/Writing_ImageJ2_plugins> in the Development >> <http://imagej.net/Development> section of the ImageJ wiki. >> >> Thanks for the interest in ImageJ2 - let us know if you have any questions >> or run into problems! >> >> Best, >> Mark >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: [ImageJ-devel] plugin development for ImageJ2 or ImageJ1?
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Hi Gerrit,
>so given the fact that ImageJ2 reached the 2.0.0 stage in june last year, and also since it is the default ImageJ version in Fiji The ImageJ welcome page [1] describes each of Fiji, ImageJ 1.x and ImageJ2 in detail. But to clarify briefly, Fiji is a distribution of ImageJ - it includes both ImageJ 1.x, and ImageJ2 (as well as a number of plugins). >So from your message I conclude that although my customer uses Fiji, I better stick to ImageJ1 Because Fiji ships both ImageJ 1.x and IJ2, it is capable of running plugins for both. Since your client can use either, for production work like it sounds you're doing, you should use the ImageJ 1.x API [2] due to its stability. The ImageJ2 team is committed to backwards compatibility with ImageJ 1.x [3], so your plugins should still work as ImageJ2 continues to develop. >Is there information available about ImageJ’s roadmap? All our development happens on GitHub [4]. In particular, the base ImageJ repository [5] provides a good view of issues and milestones. >As you suggested I will send this message also to Imagej-devel, sorry for cross-posting. No worries at all. Per the mailing list descriptions [6], both of these lists are perfectly appropriate for the scope of these discussions. Hope this helps. Thanks for the questions - let us know if you have any more! Best, Mark [1] http://imagej.net/Welcome [2] http://imagej.net/developer/api/index.html [3] http://imagej.net/Frequently_Asked_Questions#Will_ImageJ1_macros.2C_plugins_and_scripts_still_work_in_ImageJ2.3F [4] http://imagej.net/Git [5] https://github.com/imagej/imagej [6] http://imagej.net/Mailing_lists On Thu, Jan 8, 2015 at 7:16 AM, Polder, Gerrit <[hidden email]> wrote: > Dear Wayne, > > I’m a little bit confused reading ImageJ2 is still in beta. > > Im not a fulltime ImageJ user, but once and a while customers ask me to > develop imaging software in ImageJ. Mainly I'm using Matlab and Halcon. > I’m spending about 4-8 weeks a year on ImageJ. My previous project was > about a year ago. > Currently I need to update some features on one of my plugins, so given > the fact that ImageJ2 reached the 2.0.0 stage in june last year, and also > since it is the default ImageJ version in Fiji, as I already said I thought > it would be worthwhile to convert it to the current ImageJ platform, in > order to make it future proof. > > So from your message I conclude that although my customer uses Fiji, I > better stick to ImageJ1, in order not to provide him with a buggy plugin. > > On the last two conferences I’v seen a lot of nice ImageJ2 and ImgLib > features, and promises about availability. > Is there information available about ImageJ’s roadmap? > > As you suggested I will send this message also to Imagej-devel, sorry for > cross-posting. > > best regards, > Gerrit. > > On 8 Jan 2015, at 05:50, Rasband, Wayne (NIH/NIMH) [E] < > [hidden email]> wrote: > > > Dear Gerrit, > > > >> On Jan 7, 2015, at 2:54 PM, Polder, Gerrit <[hidden email]> > wrote: > >> > >> Dear Wayne, > >> > >> thanks for the prompt reply, my question was indeed not clear stated. > >> Yes this is a ImageJ1 plugin, but since I need to add some > functionality to it I thought it would be worthwhile to convert it to the > current ImageJ platform, in order to make it future proof. > >> As ImageJ2 now is the production release I decided to give it a try. > > > > ImageJ2 is not the production release. It is beta software. The two > options in Fiji’s Edit>Option>ImageJ2 dialog (ImageJ2 data structures and > SCIFIO) are disabled by default because they are buggy. > > > >> Is it true that questions related to the development of user plugins > should be addressed to imagej-devel? > > > > Question related to development of ImageJ2 plugins, imglib2 and SCIFIO > should be addressed to imagej-devel. > > > >> I’m also curious about other plugin developers, how many still develop > in ImageJ1, and how many switched already to ImageJ2? > > > > Most developers are still writing ImageJ plugins. > > > >> By the way I already found part of the problem. The Image I tested my > plugin tryout on was an old ImageJ image, instead of a new dataset ‘image’. > After enabling the SCIFIO library I could input an image in my plugin. > >> But still I think need more documentation and examples, kind of ‘guide > for switchers’. > > > > You should bring these issues up on the imagej-devel mailing list. > > > > Best regards, > > > > -wayne > > > > > >> On 7 jan. 2015, at 17:26, Rasband, Wayne (NIH/NIMH) [E] < > [hidden email]<mailto:[hidden email]>> wrote: > >> > >> Dear Polder, > >> > >> Your plugin is not an ImageJ2 plugin. It is an ImageJ plugin that you > can easily compile and run it using the Plugins>Compile and Run command. > Questions about ImageJ2 and mavin should be sent to the image-dev mailing > list. > >> > >> http://imagej.net/mailman/listinfo/imagej-devel > >> > >> Best regards, > >> > >> -wayne > >> > >> > >> > >> On Jan 7, 2015, at 10:40 AM, Polder, Gerrit <[hidden email] > <mailto:[hidden email]>> wrote: > >> > >> I succeeded in making a maven project, but I’m still struggling in > finding demo code and the api for writing a simple plugin. > >> For instance how to code a pluginfiler in imagej2? > >> > >> public class Get_blue_region implements PlugInFilter { > >> ImagePlus imp; > >> boolean DEBUG = false; > >> > >> public int setup(String arg, ImagePlus imp) { > >> this.imp = imp; > >> if (arg.equals("about")) { > >> showAbout(); > >> return DONE; > >> } > >> return DOES_RGB; > >> } > >> > >> public void run(ImageProcessor ip) { > >> ImagePlus calim = new ImagePlus("Blue Part", ip); > >> ……………. > >> } > >> } > >> > >> sorry if this is a silly question, but I got stuck in all wikis and > github repositories. > >> > >> Gerrit. > >> > >> > >> On 20 Dec 2014, at 19:11, Polder, Gerrit <[hidden email]<mailto: > [hidden email]><mailto:[hidden email]>> wrote: > >> > >> thanks Mark, this is exactly where I was looking for. > >> > >> Gerrit. > >> > >> On 20 dec. 2014, at 06:00, IMAGEJ automatic digest system < > [hidden email]<mailto:[hidden email]><mailto: > [hidden email]>> wrote: > >> > >> Hi Gerrit, > >> > >> Now I like to switch to IJ2, I’m wondering whether there is an IJ2 > example > >> project available. > >> > >> The ImageJ-tutorials <https://github.com/imagej/imagej-tutorials> > project > >> is the intended starting point for developers. There is also an > accompanying > >> entry <http://imagej.net/Writing_ImageJ2_plugins> in the Development > >> <http://imagej.net/Development> section of the ImageJ wiki. > >> > >> Thanks for the interest in ImageJ2 - let us know if you have any > questions > >> or run into problems! > >> > >> Best, > >> Mark > >> > >> -- > >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html > >> > > > > > _______________________________________________ > ImageJ-devel mailing list > [hidden email] > http://imagej.net/mailman/listinfo/imagej-devel > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Gerrit,
> I’m a little bit confused reading ImageJ2 is still in beta. It is confusing because "ImageJ2" consists of more than one component -- some of which are still in beta, and some of which are not [1]. In each case, the component's version number gives a hint [2]. In a nutshell: ImageJ2 is "in production" as an end-user application which enhances ImageJ1, but ImageJ2's data model [3] and image I/O [4] libraries are still under heavy development and not yet production quality. > I thought it would be worthwhile to convert it to the current ImageJ > platform, in order to make it future proof. As Mark said, coding against ImageJ 1.x is the most future proof for now. The ImageJ2 data model will be a good choice once it is more mature and has reached version 1.0.0. > I’v seen a lot of nice ImageJ2 and ImgLib features, and promises about > availability. If you want to start utilizing some of the new features sooner, two useful components in particular are out of beta: 1. ImgLib2 [5] - powerful new N-dimensional data model There are several Fiji plugins (e.g., [6]) that use ImgLib2 together with the ImageJ1 data model; the imglib2-ij component [7] is useful for doing this. (The difference between ImgLib2 and ImageJ2 is: ImgLib2 provides a powerful underlying image data model, while ImageJ2 builds rich metadata structures on top of it.) 2. SciJava Common [8] - powerful new plugin framework There are several cool things you can do with SciJava Common -- e.g., define new plugin types, or write parameterized commands (e.g., [9], [10]) usable from various applications such as ImageJ, KNIME, OMERO and CellProfiler. All the code is available on GitHub [11], and all the binaries are shipped with Fiji [12]. Regards, Curtis [1] http://imagej.net/ImageJ2#ImageJ2_is_more_than_just_an_application [2] http://imagej.net/Architecture#Versioning [3] http://imagej.net/ImageJ_Common [4] http://imagej.net/SCIFIO [5] http://imagej.net/ImgLib2 [6] http://fiji.sc/Stitching [7] https://github.com/imglib/imglib2-ij [8] http://imagej.net/SciJava_Common [9] http://git.io/zEx--w [10] http://git.io/FapZcw [11] http://imagej.net/Source_code [12] http://fiji.sc/Downloads On Thu, Jan 8, 2015 at 8:29 AM, Mark Hiner <[hidden email]> wrote: > Hi Gerrit, > > >so given the fact that ImageJ2 reached the 2.0.0 stage in june last > year, and also since it is the default ImageJ version in Fiji > > The ImageJ welcome page [1] describes each of Fiji, ImageJ 1.x and ImageJ2 > in detail. But to clarify briefly, Fiji is a distribution of ImageJ - it > includes both ImageJ 1.x, and ImageJ2 (as well as a number of plugins). > > >So from your message I conclude that although my customer uses Fiji, I > better stick to ImageJ1 > > Because Fiji ships both ImageJ 1.x and IJ2, it is capable of running > plugins for both. Since your client can use either, for production work > like it sounds you're doing, you should use the ImageJ 1.x API [2] due to > its stability. The ImageJ2 team is committed to backwards compatibility > with ImageJ 1.x [3], so your plugins should still work as ImageJ2 continues > to develop. > > >Is there information available about ImageJ’s roadmap? > > All our development happens on GitHub [4]. In particular, the base ImageJ > repository [5] provides a good view of issues and milestones. > > >As you suggested I will send this message also to Imagej-devel, sorry > for cross-posting. > > No worries at all. Per the mailing list descriptions [6], both of these > lists are perfectly appropriate for the scope of these discussions. > > Hope this helps. Thanks for the questions - let us know if you have any > more! > > Best, > Mark > > [1] http://imagej.net/Welcome > [2] http://imagej.net/developer/api/index.html > [3] > http://imagej.net/Frequently_Asked_Questions#Will_ImageJ1_macros.2C_plugins_and_scripts_still_work_in_ImageJ2.3F > [4] http://imagej.net/Git > [5] https://github.com/imagej/imagej > [6] http://imagej.net/Mailing_lists > > On Thu, Jan 8, 2015 at 7:16 AM, Polder, Gerrit <[hidden email]> > wrote: > >> Dear Wayne, >> >> I’m a little bit confused reading ImageJ2 is still in beta. >> >> Im not a fulltime ImageJ user, but once and a while customers ask me to >> develop imaging software in ImageJ. Mainly I'm using Matlab and Halcon. >> I’m spending about 4-8 weeks a year on ImageJ. My previous project was >> about a year ago. >> Currently I need to update some features on one of my plugins, so given >> the fact that ImageJ2 reached the 2.0.0 stage in june last year, and also >> since it is the default ImageJ version in Fiji, as I already said I thought >> it would be worthwhile to convert it to the current ImageJ platform, in >> order to make it future proof. >> >> So from your message I conclude that although my customer uses Fiji, I >> better stick to ImageJ1, in order not to provide him with a buggy plugin. >> >> On the last two conferences I’v seen a lot of nice ImageJ2 and ImgLib >> features, and promises about availability. >> Is there information available about ImageJ’s roadmap? >> >> As you suggested I will send this message also to Imagej-devel, sorry for >> cross-posting. >> >> best regards, >> Gerrit. >> >> On 8 Jan 2015, at 05:50, Rasband, Wayne (NIH/NIMH) [E] < >> [hidden email]> wrote: >> >> > Dear Gerrit, >> > >> >> On Jan 7, 2015, at 2:54 PM, Polder, Gerrit <[hidden email]> >> wrote: >> >> >> >> Dear Wayne, >> >> >> >> thanks for the prompt reply, my question was indeed not clear stated. >> >> Yes this is a ImageJ1 plugin, but since I need to add some >> functionality to it I thought it would be worthwhile to convert it to the >> current ImageJ platform, in order to make it future proof. >> >> As ImageJ2 now is the production release I decided to give it a try. >> > >> > ImageJ2 is not the production release. It is beta software. The two >> options in Fiji’s Edit>Option>ImageJ2 dialog (ImageJ2 data structures and >> SCIFIO) are disabled by default because they are buggy. >> > >> >> Is it true that questions related to the development of user plugins >> should be addressed to imagej-devel? >> > >> > Question related to development of ImageJ2 plugins, imglib2 and SCIFIO >> should be addressed to imagej-devel. >> > >> >> I’m also curious about other plugin developers, how many still develop >> in ImageJ1, and how many switched already to ImageJ2? >> > >> > Most developers are still writing ImageJ plugins. >> > >> >> By the way I already found part of the problem. The Image I tested my >> plugin tryout on was an old ImageJ image, instead of a new dataset ‘image’. >> After enabling the SCIFIO library I could input an image in my plugin. >> >> But still I think need more documentation and examples, kind of ‘guide >> for switchers’. >> > >> > You should bring these issues up on the imagej-devel mailing list. >> > >> > Best regards, >> > >> > -wayne >> > >> > >> >> On 7 jan. 2015, at 17:26, Rasband, Wayne (NIH/NIMH) [E] < >> [hidden email]<mailto:[hidden email]>> wrote: >> >> >> >> Dear Polder, >> >> >> >> Your plugin is not an ImageJ2 plugin. It is an ImageJ plugin that you >> can easily compile and run it using the Plugins>Compile and Run command. >> Questions about ImageJ2 and mavin should be sent to the image-dev mailing >> list. >> >> >> >> http://imagej.net/mailman/listinfo/imagej-devel >> >> >> >> Best regards, >> >> >> >> -wayne >> >> >> >> >> >> >> >> On Jan 7, 2015, at 10:40 AM, Polder, Gerrit <[hidden email] >> <mailto:[hidden email]>> wrote: >> >> >> >> I succeeded in making a maven project, but I’m still struggling in >> finding demo code and the api for writing a simple plugin. >> >> For instance how to code a pluginfiler in imagej2? >> >> >> >> public class Get_blue_region implements PlugInFilter { >> >> ImagePlus imp; >> >> boolean DEBUG = false; >> >> >> >> public int setup(String arg, ImagePlus imp) { >> >> this.imp = imp; >> >> if (arg.equals("about")) { >> >> showAbout(); >> >> return DONE; >> >> } >> >> return DOES_RGB; >> >> } >> >> >> >> public void run(ImageProcessor ip) { >> >> ImagePlus calim = new ImagePlus("Blue Part", ip); >> >> ……………. >> >> } >> >> } >> >> >> >> sorry if this is a silly question, but I got stuck in all wikis and >> github repositories. >> >> >> >> Gerrit. >> >> >> >> >> >> On 20 Dec 2014, at 19:11, Polder, Gerrit <[hidden email]<mailto: >> [hidden email]><mailto:[hidden email]>> wrote: >> >> >> >> thanks Mark, this is exactly where I was looking for. >> >> >> >> Gerrit. >> >> >> >> On 20 dec. 2014, at 06:00, IMAGEJ automatic digest system < >> [hidden email]<mailto:[hidden email]><mailto: >> [hidden email]>> wrote: >> >> >> >> Hi Gerrit, >> >> >> >> Now I like to switch to IJ2, I’m wondering whether there is an IJ2 >> example >> >> project available. >> >> >> >> The ImageJ-tutorials <https://github.com/imagej/imagej-tutorials> >> project >> >> is the intended starting point for developers. There is also an >> accompanying >> >> entry <http://imagej.net/Writing_ImageJ2_plugins> in the Development >> >> <http://imagej.net/Development> section of the ImageJ wiki. >> >> >> >> Thanks for the interest in ImageJ2 - let us know if you have any >> questions >> >> or run into problems! >> >> >> >> Best, >> >> Mark >> >> >> >> -- >> >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> >> >> > >> >> >> _______________________________________________ >> ImageJ-devel mailing list >> [hidden email] >> http://imagej.net/mailman/listinfo/imagej-devel >> > > > _______________________________________________ > ImageJ-devel mailing list > [hidden email] > http://imagej.net/mailman/listinfo/imagej-devel > > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Curtis and Mark,
thanks for clarifying the situation. As I already told I’m an occasional ImageJ user/programmer, and due to that not completely up to date regarding its current stage. Regarding ImageJ2 versus ImgLib, yes I know, I joined one of the ImgLib workshops during the last ImageJ conference in Luxembourg. This is one of the reasons I really would like to switch. But your explanation placed me with both feet again on the ground. For this particular project I will use ImageJ1. Best regards, Gerrit. On 8 jan. 2015, at 20:57, Curtis Rueden <[hidden email]<mailto:[hidden email]>> wrote: Hi Gerrit, > I’m a little bit confused reading ImageJ2 is still in beta. It is confusing because "ImageJ2" consists of more than one component -- some of which are still in beta, and some of which are not [1]. In each case, the component's version number gives a hint [2]. In a nutshell: ImageJ2 is "in production" as an end-user application which enhances ImageJ1, but ImageJ2's data model [3] and image I/O [4] libraries are still under heavy development and not yet production quality. > I thought it would be worthwhile to convert it to the current ImageJ > platform, in order to make it future proof. As Mark said, coding against ImageJ 1.x is the most future proof for now. The ImageJ2 data model will be a good choice once it is more mature and has reached version 1.0.0. > I’v seen a lot of nice ImageJ2 and ImgLib features, and promises about > availability. If you want to start utilizing some of the new features sooner, two useful components in particular are out of beta: 1. ImgLib2 [5] - powerful new N-dimensional data model There are several Fiji plugins (e.g., [6]) that use ImgLib2 together with the ImageJ1 data model; the imglib2-ij component [7] is useful for doing this. (The difference between ImgLib2 and ImageJ2 is: ImgLib2 provides a powerful underlying image data model, while ImageJ2 builds rich metadata structures on top of it.) 2. SciJava Common [8] - powerful new plugin framework There are several cool things you can do with SciJava Common -- e.g., define new plugin types, or write parameterized commands (e.g., [9], [10]) usable from various applications such as ImageJ, KNIME, OMERO and CellProfiler. All the code is available on GitHub [11], and all the binaries are shipped with Fiji [12]. Regards, Curtis [1] http://imagej.net/ImageJ2#ImageJ2_is_more_than_just_an_application [2] http://imagej.net/Architecture#Versioning [3] http://imagej.net/ImageJ_Common [4] http://imagej.net/SCIFIO [5] http://imagej.net/ImgLib2 [6] http://fiji.sc/Stitching [7] https://github.com/imglib/imglib2-ij [8] http://imagej.net/SciJava_Common [9] http://git.io/zEx--w [10] http://git.io/FapZcw [11] http://imagej.net/Source_code [12] http://fiji.sc/Downloads On Thu, Jan 8, 2015 at 8:29 AM, Mark Hiner <[hidden email]<mailto:[hidden email]>> wrote: Hi Gerrit, >so given the fact that ImageJ2 reached the 2.0.0 stage in june last year, and also since it is the default ImageJ version in Fiji The ImageJ welcome page [1] describes each of Fiji, ImageJ 1.x and ImageJ2 in detail. But to clarify briefly, Fiji is a distribution of ImageJ - it includes both ImageJ 1.x, and ImageJ2 (as well as a number of plugins). >So from your message I conclude that although my customer uses Fiji, I better stick to ImageJ1 Because Fiji ships both ImageJ 1.x and IJ2, it is capable of running plugins for both. Since your client can use either, for production work like it sounds you're doing, you should use the ImageJ 1.x API [2] due to its stability. The ImageJ2 team is committed to backwards compatibility with ImageJ 1.x [3], so your plugins should still work as ImageJ2 continues to develop. >Is there information available about ImageJ’s roadmap? All our development happens on GitHub [4]. In particular, the base ImageJ repository [5] provides a good view of issues and milestones. >As you suggested I will send this message also to Imagej-devel, sorry for cross-posting. No worries at all. Per the mailing list descriptions [6], both of these lists are perfectly appropriate for the scope of these discussions. Hope this helps. Thanks for the questions - let us know if you have any more! Best, Mark [1] http://imagej.net/Welcome [2] http://imagej.net/developer/api/index.html [3] http://imagej.net/Frequently_Asked_Questions#Will_ImageJ1_macros.2C_plugins_and_scripts_still_work_in_ImageJ2.3F [4] http://imagej.net/Git [5] https://github.com/imagej/imagej [6] http://imagej.net/Mailing_lists On Thu, Jan 8, 2015 at 7:16 AM, Polder, Gerrit <[hidden email]<mailto:[hidden email]>> wrote: Dear Wayne, I’m a little bit confused reading ImageJ2 is still in beta. Im not a fulltime ImageJ user, but once and a while customers ask me to develop imaging software in ImageJ. Mainly I'm using Matlab and Halcon. I’m spending about 4-8 weeks a year on ImageJ. My previous project was about a year ago. Currently I need to update some features on one of my plugins, so given the fact that ImageJ2 reached the 2.0.0 stage in june last year, and also since it is the default ImageJ version in Fiji, as I already said I thought it would be worthwhile to convert it to the current ImageJ platform, in order to make it future proof. So from your message I conclude that although my customer uses Fiji, I better stick to ImageJ1, in order not to provide him with a buggy plugin. On the last two conferences I’v seen a lot of nice ImageJ2 and ImgLib features, and promises about availability. Is there information available about ImageJ’s roadmap? As you suggested I will send this message also to Imagej-devel, sorry for cross-posting. best regards, Gerrit. On 8 Jan 2015, at 05:50, Rasband, Wayne (NIH/NIMH) [E] <[hidden email]<mailto:[hidden email]>> wrote: > Dear Gerrit, > >> On Jan 7, 2015, at 2:54 PM, Polder, Gerrit <[hidden email]<mailto:[hidden email]>> wrote: >> >> Dear Wayne, >> >> thanks for the prompt reply, my question was indeed not clear stated. >> Yes this is a ImageJ1 plugin, but since I need to add some functionality to it I thought it would be worthwhile to convert it to the current ImageJ platform, in order to make it future proof. >> As ImageJ2 now is the production release I decided to give it a try. > > ImageJ2 is not the production release. It is beta software. The two options in Fiji’s Edit>Option>ImageJ2 dialog (ImageJ2 data structures and SCIFIO) are disabled by default because they are buggy. > >> Is it true that questions related to the development of user plugins should be addressed to imagej-devel? > > Question related to development of ImageJ2 plugins, imglib2 and SCIFIO should be addressed to imagej-devel. > >> I’m also curious about other plugin developers, how many still develop in ImageJ1, and how many switched already to ImageJ2? > > Most developers are still writing ImageJ plugins. > >> By the way I already found part of the problem. The Image I tested my plugin tryout on was an old ImageJ image, instead of a new dataset ‘image’. After enabling the SCIFIO library I could input an image in my plugin. >> But still I think need more documentation and examples, kind of ‘guide for switchers’. > > You should bring these issues up on the imagej-devel mailing list. > > Best regards, > > -wayne > > >> On 7 jan. 2015, at 17:26, Rasband, Wayne (NIH/NIMH) [E] <[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote: >> >> Dear Polder, >> >> Your plugin is not an ImageJ2 plugin. It is an ImageJ plugin that you can easily compile and run it using the Plugins>Compile and Run command. Questions about ImageJ2 and mavin should be sent to the image-dev mailing list. >> >> http://imagej.net/mailman/listinfo/imagej-devel >> >> Best regards, >> >> -wayne >> >> >> >> On Jan 7, 2015, at 10:40 AM, Polder, Gerrit <[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>>> wrote: >> >> I succeeded in making a maven project, but I’m still struggling in finding demo code and the api for writing a simple plugin. >> For instance how to code a pluginfiler in imagej2? >> >> public class Get_blue_region implements PlugInFilter { >> ImagePlus imp; >> boolean DEBUG = false; >> >> public int setup(String arg, ImagePlus imp) { >> this.imp = imp; >> if (arg.equals("about")) { >> showAbout(); >> return DONE; >> } >> return DOES_RGB; >> } >> >> public void run(ImageProcessor ip) { >> ImagePlus calim = new ImagePlus("Blue Part", ip); >> ……………. >> } >> } >> >> sorry if this is a silly question, but I got stuck in all wikis and github repositories. >> >> Gerrit. >> >> >> On 20 Dec 2014, at 19:11, Polder, Gerrit <[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>><mailto:[hidden email]<mailto:[hidden email]>>> wrote: >> >> thanks Mark, this is exactly where I was looking for. >> >> Gerrit. >> >> On 20 dec. 2014, at 06:00, IMAGEJ automatic digest system <[hidden email]<mailto:[hidden email]><mailto:[hidden email]<mailto:[hidden email]>><mailto:[hidden email]<mailto:[hidden email]>>> wrote: >> >> Hi Gerrit, >> >> Now I like to switch to IJ2, I’m wondering whether there is an IJ2 example >> project available. >> >> The ImageJ-tutorials <https://github.com/imagej/imagej-tutorials> project >> is the intended starting point for developers. There is also an accompanying >> entry <http://imagej.net/Writing_ImageJ2_plugins> in the Development >> <http://imagej.net/Development> section of the ImageJ wiki. >> >> Thanks for the interest in ImageJ2 - let us know if you have any questions >> or run into problems! >> >> Best, >> Mark >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > _______________________________________________ ImageJ-devel mailing list [hidden email]<mailto:[hidden email]> http://imagej.net/mailman/listinfo/imagej-devel _______________________________________________ ImageJ-devel mailing list [hidden email]<mailto:[hidden email]> http://imagej.net/mailman/listinfo/imagej-devel -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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