Need BAR/Distribution Plotter plugin for ImageJ not Fiji

imagej
plugin

#1

I attempted to download the Distribution Plotter plugin but, was unable to locate this isolated plugin on GitHub. I primarily work in ImageJ yet, use both ImageJ and Fiji. However, all my work relevant to this current project has been performed in ImageJ and it does not offer the ability to “Manage Update Sites” as Fiji does. How can I obtain BAR for ImageJ? In the event ImageJ does offer this update feature, I have forgotten how to enable it. Please advise.


#2

Good day Rick,

installing plugins in ImageJ is easy and no update site management is required (it doesn’t even exist).

Locate either the Java source code /(suffix “.java”) and compile it via “Plugins >> Compile and Run…” or, if you are lucky, you may find an already compiled plugin (suffix “.class” or “.jar”) and place it in the plugins folder of your ImageJ installtion and restart ImageJ.

If however, the plugin in question is based on ImageJ-2 and related technique, you won’t be able to run it with plain ImageJ.

Regards

Herbie

PS:
Distribution_Plotter.ijm
is not a plugin but an ImageJ-macro that runs as is.
Don’t know if it requires certain plugins to function …


#3

@RVC,

The source code is all on GitHub, organized under the same directory structure you find in the BAR> menu. Distribution Plotter is in BAR>Analysis> so you will find all the source files under the Analysis directory: Here are the links for Analysis scripts, and Distribution_Plotter.ijm.

Distribution_Plotter.ijm is an IJ1 macro, so it will be functional for the most part without the BAR “infrastructure”, but be warned that some extra-functionality will be curbed: E.g., in BAR when you run Distribution Plotter and it does not find input data, the macro will try to gather a valid input before exiting by calling compiled java classes that will not be available outside the BAR update site (unless you manually copy them), so you may want to, e.g., modify this line in the macro to something more relevant.


#4

@Herbie, @tferr - Thank you both for the prompt and useful responses. I can run with this information and see how far I get with it. If necessary, I may need to migrate this project to Fiji…working with both applications can be inconvenient.

Rick


#5

BTW, the Distribuition Plotter macro was written several years ago so that one could plot conveniently histograms in IJ, meanwhile thanks to remarkable work on @schmid, you have a direct API for assembling histograms.

It shouldn’t have to be, have a look at the FAQs. I’m sure you will find some useful information there.


#6

Just for clarification, the API and function for plotting histograms (Plot.addHistogram) was created by Norbert Vischer, not me.
It is still rather basic; not really comparable to the fancy Distribution Plotter of BAR.
E.g. only one method for auto bins, values are not written to the plot, no cumulative frequencies (integrated distribution), and no automatic Gaussian fit.
– Michael


#7

@schmid - I am grateful for your response here. This provides me with direction and saves me a lot of work using a tool that will not provide what I need.

Thank you Michael, I will have to migrate this project to Fiji in view of this new information.