Strawberry seed counting - help?

Hi,
We have over 1000 scans of flattened strawberries and are looking for an efficient way to estimate the number of seeds, and hopefully get a distribution of the seed sizes for each strawberry. We’re hoping cellprofiler could do the trick. ANY help or advice to get started would be greatly appreciated !!! Ie. pipelines to consider? editing methods? feasibility?

The modules we’ve been experimenting with:
Invert intensity
Identify primary objects
Measure object area shape
Exporting

Greatest challenge we’ve been facing: identifying the seeds! Would it be best to hand edit all the files in photoshop so there are only white seeds on a fully black background (without any strawberry flesh). Or can cellprofiler allow us to identify seeds (maybe with intensity, threshhold, etc?) with some level of accuracy.

Thanks in advance! :smiley:

  • FC (UC Berkeley undergrad research assistant)

Sample of what a strawberry scan looks like attached (1 original, 1 inverted in photoshop with curves… we could do other manipulations as needed!)




Hi!

I’ve made a simple attempt to solve your problem. The segmentation is fairly good, but you will have to tweak it a little bit. Also, there are other objects than seed being detected, but they can be filtered out. I’ve used only formfactor to take out all the objects that aren’t more or less circular. I think you should use CPAnalyst to find better rules to filter out the non-seed objects in the image. Any doubts, just aks!

Best Regards,

Roberto
TEST.cp (7.54 KB)

Hi FC,

I’ve attached a pipeline which should point you in the right direction. There is still some more tweaking that needs to be done, but check the module notes at the top of the settings panel to see my thought process.

EDIT: I didn’t notice that rnicholas also attempted to solve the problem before I posted. Give both pipelines a try!

Hope this helps!
-Mark
2012_09_25.cp (10.8 KB)

Thanks very much to you both (Mark and Roberto) for tackling this. I am going to try both of your suggestions today to see how it goes and will keep you posted!

Finally got around to playing around with the pipelines… Thanks again for giving me great pipeline foundations!!
Roberto, I am having trouble getting your pipeline to completion due to “memory errors” - is this simply because of the computer I am using or is there something I can possibly tweak to make it go all the way through?

  • Flora