ImageJ Macro + Markdown

Imagine interactive plots with this, WebGL style :grinning:

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You’re welcome to contribute to the project :wink:

Thanks, but right now I wouldn’t know where to start with features like this or exporting to PDF. Just give me some time… for now I’m more than happy enough with static plots of Histogram or Plot Profile!

PS. minor detail, should this be and a bullet point?

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It looks great, I used the resulting markdown as a readme for a tuto subfolder of a project, very cool !

2 minor improvements I can suggest

  • the script parameters generate an empty code cell, example
    #@ImagePlus (Label="Image") image


  • Having the syntax color coding would be great (both for the preview and on GitHub).
    I am not surprised that GitHub does not recognize an ijm extension but maybe they would be open for discussion too !
    I know that @Kota made a plugin for the notepad++ and vim to have the syntax coloring for ijm. See

EDIT: by specifying java after the ``` code block it already looks better. Could it be automatic ?


Hey @LThomas,

awesome, thanks for immediately trying! And thanks for the feedback. I just changed it and put syntax highlighting for “java” there for default, as there is no “macro” language support defined, afaik.

We could change the html-generator, but that might be a lot of effort.

Alternatively, I’d recommend you to upload the .md file to github and not the html file. You can then use github pages to apply custom designs. Very flexible and less effort on our side :wink:

Just as an example one of my md files on github looks like this (pretty greyish):

The same md file rendered via (github pages) looks like this (a bit more colour):

You can try the new java-highlighting out - just add the IJMMD update site in your Fiji :wink:

Thanks again for your feedback!


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I’m just realising - you did upload the md file - you just named it readme :laughing: my fault :wink:

I’m not seeing any syntax highlighting with imagejmacromarkdown_-0.3.0
How does it work exactly? It adds the syntax highlighted fences in at runtime?
Do you have an example macro that it works with?

I always thought javascript was the one to use for syntax highlighting :slight_smile:

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Hey @camlloyd,

unfortunately, the syntax highlighting only works when the .md files is rendered through github. See examples above. I’d assume that most other markdown renderers can do it. The used markdown-html renderer cannot do it apparently.

That’s the macro from the screenshots linked above.

:man_shrugging: Wasn’t aware. Shall we make this configurable?

Now I understand.

I don’t know if it is necessary to make it configurable, but perhaps someone who knows more about this can advise what would be best!

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Hey Robert I have another idea, maybe not for the near future but still :stuck_out_tongue:

I was wondering if one could use the functionality to generate automatic reports like in KNIME (see reporting user guide )

There you can choose what to put in the report, also in jupyter notebook you can have now tag for cells (see this)

On the long run, imagine running some batch processing and for every run get such pre-formatted Markdown report :crazy_face: How cool would that be !

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