Create a scatterplot of cell measurements in QuPath v0.2.0

QuPath-Cell scatterplot.groovy

/**
 * Example showing how to create an interactive scatterplot for the cells in the current viewer
 * in QuPath v0.2.0.
 * 
 * 'Interactive' here means that double-clicking a point on the scatterplot selects the specific cell.
 * 
 * Warning! This is an early, work-in-progress feature subject to change in future releases.
 * It is *not* suitable for very large numbers of cells, because each point on the scatterplot is 
 * rather 'heavy'. It should work fine with thousands of cells, but not with hundreds of thousands.
 *
 * @author Pete Bankhead
 */

def viewer = getCurrentViewer()
def cells = getCellObjects()
def builder = Charts.scatterChart()
    .viewer(viewer)
    .title('My scatterplot')
    .measurements(cells, 'Nucleus: Area', 'Nucleus: DAB OD mean')
    .markerOpacity(0.5)
    .show()

// Uncomment the following line to get more info about available options
// println describe(Charts.scatterChart())

Ok great ! In term of delay any idea when you project to do it, I mean in a year or before ? Cheers, Mathieu

I think you're referring to a scatterplot with gating? https://forum.image.sc/t/scatterplot-cells-population/76123

No timeframe yet, I'm afraid. Gating with 2 thresholds is easier than using an arbitrary polygon (I even once wrote a script for that, but it's so long ago that I no longer know where it is...).

The forum is a better place to discuss it, and you might find other useful phenotyping tools there that are compatible with QuPath.

ok a cross threshold will be already very useful, it exist some librtary in java to do it you might know probably : https://forum.image.sc/t/javafx-scatter-plot-for-imagej-a-working-example/51368