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:
Identify primary objects
Measure object area shape
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!
- 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!)