[ImageJ-devel] plot window support

Johannes Schindelin Johannes.Schindelin at gmx.de
Tue Apr 10 15:04:23 CDT 2012

Hi Jay,

On Tue, 10 Apr 2012, Unruh, Jay wrote:

> So if there is no intrinsic plotting utility, is there any way to access
> plots (or their data) from macros or plugins?  That is perhaps my main
> complaint about using JFreeChart (that and no log axes for some reason).
> I currently use my own version of Wayne's PlotWindow which I then access
> from other plugins via reflection (not the best way, I know).  Wayne
> doesn't want to support it because of lack of backward function
> compatibility, but perhaps IJ2 is an opportunity to implement this in a
> more robust manner.  This approach has been very rewarding.  For
> example, I can do some really cool things like create dynamic histograms
> where I can change the bin size on the fly, visualize thresholds via a
> 1D or 2D histogram, etc.  It becomes easy to implement some of the
> gating that people use for cytometry analysis for example.  Anyway, not
> sure if IJ2 is the place for this kind of development, but it is an
> intriguing possibility.

In my opinion, ImageJ2 is exactly the best place to put your work into.
Because of the separation between data and UI, you will have less trouble
with backwards-compatibility. We also tried to follow the plugin pattern
where you can add different consumers; in this particular case, one could
come up with a Plot window that is written in pure AWT (like IJ1's) but
one could also use a Plot window that attaches to your Spreadsheet program
and uses that for displaying the Plot. This is possible simply because the
UI cannot affect the way the data are stored.

Of course, this flexibility comes at the price that we had to flesh out
quite a few issues "under the hood". So we did not come to work on
histograms and plot windows quite yet. But we will, hopefully with your


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