Creating a binary mask of the Convex hull of multiple particle

FS.022-C_1434.tif (1.8 MB) FS.022-C_1435.tif (1.8 MB) FS.022-C_1436.tif (1.8 MB) Hi,

I would like to create an image mask of the convex hulls of multiple particles within an image stack but cant seem to find a function/plugin that will d the job. I can get a selection of the convex hull for individual particles by Edit–> Selection–> Convex hull, then create a binary mask by Filling the Selection (Edit --> Fill). However, each image has 10’s - 100’s of individual particles and I have ~20,000 images, so doing it one-by-one would be a nightmare!! If anyone has any suggestions then it would be much appreciated.

Thanks,
John

Hi @Jonny251990,

A 3D Convex hull plugin is available part of the3D image Suite in Analysis section. It is based on quickhull3d and will take as input a labelled image and output a labelled image with convex hulls for all objects.

Best,

Thomas

Hi,
Thanks for the suggestion, I did come across the 3D Convex hull in the 3D Image Suite plugin (I’ve used it before and its very useful!) but I am actually working with 2D, not 3D data. I have a stack of 2D images with multiple particles that I want to analyse. I realise that saying ‘image stack’ may have been a bit misleading.

(I have uploaded 3 example images to the original post, the data is from a movie of particles settling out of suspension).

Thanks,
John

Although this seems straigth-forward by writing a macro that uses Analyze Particles, adds the results to the Roi Manager and/or uses the commands doWand() and run(“Convex Hull”) in a macro obtaining the XY centers of the detected particle as arguments, you might want to take care of the exceptions too; some ‘particles’ seem to have exploded, notably a particle at (733,591) in image FS.022-C_1434.tif

Is it your intention to (automatically) detect these three particles in close proximity as one?

Hi @Jonny251990,

Ah ok, actually I tried the 3D convex hull on your 2D images and it is working fine. You may need however to remove very small objects (with only a couple of pixels), else the computation of convex hull will crash.


Best,

Thomas