Counting Beans

Hi everyone,

thanks for this great tool, if I only knew how to use it.

I would like to use it to count beans and measure the surface, but I came across a few problems putting together my pipeline.

  1. seeds lying closely together are identified as one big object (as shown in attached picture
    ). I’ve been playing with all options I could find, but without much success, I’m not sure if it is a problem with the threshold or with distinguishing clumped objects.
  2. the variation in color is proving to be difficult, especially white beans are often not captured. I thought about making two analyses of different images of the split color-to -greyscale results. is there a merge function to combine these two analyses for object identification?

I hope someone has a good idea for me.
Thanks a lot,

the beancounter

Hi beancounter,
Would you mind posting a couple of example images, so we could take a look?

I thought I did.
Or do you mean the original fotos?

here are two:

the edge enhancement function actually captures the shapes very well. But I didn’t find a way to use this for the object calling.


This is not an easy problem, at least for what CellProfiler was designed for. Please see my attached pipeline, at least for some ideas on how to attack this.

  • Crop the wasted pixels if at all possible, or at least reduce the resolution. CP may run into memory errors otherwise in any filtering step.
  • Unmix Colors is meant for histological images, but seems to do ok here. You might also try the Methyl green setting.
  • I tried EnhanceOrSuppressFeatures, but you could remove this, as the EnhanceEdges seemed to work better. Either of these has the added benefit of removing the substantial background illumination artifact.
  • IdentifyPrimaryObjects - You will need to adjust the declumping parameters.

Better, though, would be to use a black background for your images if at all possible. Our thresholding assumes that the intensity of the grayscale foreground will be higher than the background. Also, there is a substantial illumination variation, which you can alleviate by CorrectIllumination[Calculate/Apply], but it’s better to minimize it depending on your light source.

DLpipeline.cppipe (7.27 KB)