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 <hi...@wisc.edu> 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 <gerrit.pol...@wur.nl> > 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] < >> rasba...@mail.nih.gov> wrote: >> >> > Dear Gerrit, >> > >> >> On Jan 7, 2015, at 2:54 PM, Polder, Gerrit <gerrit.pol...@wur.nl> >> 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] < >> rasba...@mail.nih.gov<mailto:rasba...@mail.nih.gov>> 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 <gerrit.pol...@wur.nl >> <mailto:gerrit.pol...@wur.nl>> 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 <gerrit.pol...@wur.nl<mailto: >> gerrit.pol...@wur.nl><mailto:gerrit.pol...@wur.nl>> wrote: >> >> >> >> thanks Mark, this is exactly where I was looking for. >> >> >> >> Gerrit. >> >> >> >> On 20 dec. 2014, at 06:00, IMAGEJ automatic digest system < >> lists...@list.nih.gov<mailto:lists...@list.nih.gov><mailto: >> lists...@list.nih.gov>> 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 >> ImageJ-devel@imagej.net >> http://imagej.net/mailman/listinfo/imagej-devel >> > > > _______________________________________________ > ImageJ-devel mailing list > ImageJ-devel@imagej.net > http://imagej.net/mailman/listinfo/imagej-devel > >
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