Segmentation of beads

cellprofiler

#1

Hello everyone,

This post is a bit different than the regular cell oriented questions, but I found previous posts of people trying to segment beads!:
i am trying to segment beads using bright field and to obtain outlines as circular as possible. I played around for a while with my microscope settings and different ways to segment without any satisfying and reproducible results.
So i was thinking if by a ‘quite easy’ trick, it could be possible to add pre-defined circular masks (with a specific diameter corresponding to the beads) around pre-defined regions of your images. I thought about the function shrink-expand but if my starting object isn’t round, i won’t get a circle at the end.
Hopefully this issue is clear enough and that you have some hints to share!
Thanks,

/Laurent


#2

Hi,
Have you tried an illumination correction (on the bright field images) before trying to identify the beads? Also, in IdentifyPrimAutomatic, you can use ‘shape’ as an option. (‘Shape’ tends to work well with round objects.) Also, if you need to create a mask, you can use the MaskImage module to mask your identifed beads. Indeed, the ExpandOrShrink will not work well if your objects are not identified properly from IdentifyPrimAutomatic.

Another alternative would be to try to smooth the image using the Smooth module on an inverted image and select ‘RemoveBrightRoundSpeckles’. Then try to subtract the smoothed image from the Illum Corrected image. This might help enhance your beads, thus making IdPrimAuto work better.

If these suggestions do not work, please post the images on a public photo album (ie picasaweb) and then post a link on the forum for us.

Good luck!