OMEVisual : A Fiji plugin to easily visualize OME metadata

ome
plugin

#1

I have released a new plugin to easily visualized OME Metadata when an OME TIFF file is opened in Fiji.

See on GitHub : https://github.com/hadim/OMEVisual
And on the Wiki : http://imagej.net/OMEVisual

Any comments are welcome.

A screenshot :


#2

The plugin interface uses JavaFX which is not shipped with Fiji. So you will need to replace the JVM used by Fiji with another one containing JavaFX.

For now JavaFX is only provided by the Oracle JVM (don’t ask me why it’s not integrated with OpenJDK I really don’t know…).

I am working on a easier way to run OMEVisual.


#3

In fact the Java version shipped with Fiji (for Windows 64 at least) seems to contain JavaFX because the plugin work out of the box.


#4

This rocks! :guitar: :metal: :grin:

Great. You can check using the “Find Jar for Class” command, and specifying javafx.scene.Scene. It will report if (and where) JavaFX lives in your ImageJ environment.

Each image contains only one Pixels element.

Yeah, always true these days. Always.

Each TiffData contains only one Plane.

Not always true, unfortunately…

Plane and TiffData informations are displayed at the same location without distinction.

If you want, I can try to dig up a counterexample dataset for you to play with. Just let me know.


#5

Thank you.

Sure if you have an example of OME TIFF with multiples planes by TiffData I can certainly add a third panel on the right to differentiate TiffData and Plane elements.

Do you think it’s worth adding this plugin to the Fiji distribution ? I will maintain it of course.


#6

I would like that very much.
What became of this @hadim ?


#7

I am still willing to do that. There is two possibilities here:

  • I create an update site so it’s easy to install for people.

  • @ctrueden integrates it to Fiji as a default plugin and I will maintain it.

Considering how small the plugin is, I will prefer option 2. It’s up to @ctrueden to decide.


#8

I have updated the repo, travisify it and release new versions. The jar files are available on Maven now.

Let’s wait for @ctrueden to know what to do next.


#9

@hadim As long as the plugin meets the Fiji contribution requirements, and you will maintain it, then adding it to Fiji would be great. Steps:

  • File a PR to pom-scijava adding it to the BOM as a managed component.
  • Merge the PR & release a new version of pom-scijava.
  • File a PR against fiji/fiji updating the version of pom-scijava and adding OMEVisual as a runtime dependency.
  • File a PR against fiji/fiji-javadoc adding OMEVisual to the javadocs.
  • Upload OMEVisual to the Java-8 update site.

You can likely perform most of these steps yourself, without my help.


#10

Here is the PR for pom-scijava: https://github.com/scijava/pom-scijava/pull/55

I don’t have the permission to merge it so I’ll rely on you for that and for the other PRs too.

Thanks @ctrueden.