Identifying/Measuring collagen fiblrils

I hope someone may have an answer for this, I’m too new to this program to tell if the issue is with the program or user error. Basically what we’re trying to do is measure the number and diameter/area of collagen fibrils from EM images. There’s some examples below. The pipeline I used was Smooth–>Threshold–>ImageMath (to invert)–>IdentifyPrimaryObjects. Because of the variability in the images (the fibrils can be spaced apart, or packed tightly together, and the EM pics vary in contrast) the IdentifyPrimaryObjects module keeps splitting up the fibrils into multiple objects, and not properly detecting the fibrils from the background. Is there any help or advice anyone here could give? I’d really appreciate it, there are a lot of parameters to play with, and none of the downloadable examples seem to fit.

Thanks,
-S Watson




Hi,

I’m attaching a pipeline which should get you started; some more tweaking is needed in the fibril identification step though. Basically, I did the following (see the module notes for further details):

  • Mask the image to get rid the dark background
  • Do some illumination correction for better detection
  • Optimize parameters for fibril detection
  • Make measurements and export data

Hope this helps!
-Mark
2010_08_23.cp (8.14 KB)

That works a LOT better. Thanks so much, that is a huge help!

-S Watson