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Howto - Authoring a page

    GitHub pages and Jekyll

    Click here to learn more about GitHub pages. Click here to learn more about Jekyll.

    Getting started

    Creating or editing a page on GitHub pages is super easy! Pages can be created or modified online via GitHub’s online file editor (clicking “Edit page” on the top right of this page will bring you to this specific page’s source) or via a local installation of jekyll and the imagej.github.io site. We recommend installing jekyll and generating the site locally. The advantage of this is that changes can be viewed very quickly without pushing code up to GitHub and waiting for the site to render. This process is slow espcially if you just simply want to check how your page is rendering so far.

    Setup a local jekyll installation (optional)

    The jekyll static site generator can be installed on Linux, MacOS and Windows. To install a local version of jekyll follow the instructions for your respective operating system here. Once jekyll has been installed, clone the the imagej.github.io repository. Navigate to the cloned repository and run bundle install to install the specific gems used in imagej.github.io. Once this is complete you can run the static site generator by navigating where imagej.github.io was saved to and running bundle exec jekyll serve. Wait for a minute or two while it generates and then in your browser navigate to http://127.0.0.1:4000. Any changes you make to any file in the directory will be detected by jekyll, regenerating the site to reflect the new changes.

    Page - front matter

    Page - content

    Page - using includes

    Avaliable “includes”

    Action Link to demo page
    Insert the about menu about-menu
    Insert conference info conference
    Generate info/details box details-box
    Insert figure figure
    Insert a gallery gallery
    Link to github files github
    Insert Git menu git-menu
    Insert images image
    Insert a notice info-box
    Insert logos logo
    Insert menu breadcrumb menu-bc
    Insert math math
    Insert person details person
    Insert a sidebox sidebox
    Insert the SNT nav bar SNT-nav
    Insert a tech box tech-box
    Insert a warning warning-box

    Introduction


    While in Clojure one is able to declare types if desired, it’s not required; the low computational requirements of the plugin do not invite to make it verbose unnecessarily. But java demands type declarations just so that the plugin can be compiled and thus a binary .class file generated.

    While in Clojure one is able to declare types if desired, it’s not required; the low computational requirements of the plugin do not invite to make it verbose unnecessarily. But java demands type declarations just so that the plugin can be compiled and thus a binary .class file generated.

    Figure center


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    Figure 3 : This is a center figure.

    While both the java and clojure versions encapsulate the variables in a local namespace -in Clojure, by using let statements to declare local variables-, the jython version does not, so they are all global when defined outside the class definition. One can achieve, though, variable encapsulation by declaring the entire script inside a class or function definition -but its not required as in java, neither as natural and straightforward as in Clojure.

    While both the java and clojure versions encapsulate the variables in a local namespace -in Clojure, by using let statements to declare local variables-, the jython version does not, so they are all global when defined outside the class definition. One can achieve, though, variable encapsulation by declaring the entire script inside a class or function definition -but its not required as in java, neither as natural and straightforward as in Clojure.

    Figure row


    While both the java and clojure versions encapsulate the variables in a local namespace -in Clojure, by using let statements to declare local variables-, the jython version does not, so they are all global when defined outside the class definition. One can achieve, though, variable encapsulation by declaring the entire script inside a class or function definition -but its not required as in java, neither as natural and straightforward as in Clojure.

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    Markdown table


    Item 1 Item 2 Item 3
    A B C
    1 2 3

    YouTube video


    Embedded images in table


    A table with images, use the .image.table to make it align with text:

    Plugins A powerful mechanism for extending ImageJ in all kinds of useful ways.
    Extend Automated, reproducible workflows via scripts and macros, including headless on a remote server or cluster.

    Syntax highlighting


    Java example:

    Image3DUniverse univ = new Image3DUniverse();
    univ.show();
    univ.addMesh(yourImagePlus, null, "somename", 50, new boolean[] {true, true, true}, 2);
    ...
    

    Python example:

    def update_progress(progress):
        barLength = 10 # Modify this to change the length of the progress bar
        status = ""
        if isinstance(progress, int):
            progress = float(progress)
        if not isinstance(progress, float):
            progress = 0
            status = "error: progress var must be float\r\n"
        if progress < 0:
            progress = 0
            status = "Halt...\r\n"
        if progress >= 1:
            progress = 1
            status = "Done...\r\n"
        block = int(round(barLength*progress))
        text = "\rPercent complete: [{0}] {1}% {2}".format( "#"*block + "-"*(barLength-block), progress*100, status)
        sys.stdout.write(text)
        sys.stdout.flush()