Displaying millions of Point Roi - very slow


I am currently working with a point cloud that delimitates a surface in a 3D stack. My point cloud contains up to 10 millions points and the stack is 7.5 GB (4136x3120x626).

I usually draw the point cloud within the stack by overlaying it with as many Roi point as required. Above a million point, ImageJ starts to be very slow, and I reach the “unusability limit”.

Do you if there is a way to draw such a point cloud within the stack, (without modifying the data of the original stack) ?

Thanks for your suggestions,


So I went through the piece of ImageJ1 code that displays Overlay. It is here : https://github.com/imagej/imagej1/blob/master/ij/gui/ImageCanvas.java#L285

Basically each time the user changes the position displayed within the stack, a loop is made through all overlay elements. This means, if I understand correctly, that there is no pre-sorting of overlays based on their position within the stack (z, channel or timepoints). Hence the slow display.

I guess this will behaviour will be rather complicated to modify without consequent rewriting.

1 Like