Streptomyces image analysis using Trainable meka segmentation

Hello

I have multiple of these streptomyces images grown in growth chambers. I would like to segment them from the growth chamber. I thought the trainable meka segmentation might be the best for this? Given how they look is there a good way to tune the training parameters? Once i have achieved a good segmentation I would like to extract the tips and branches. Is the skeletonize tool the best for this?

Thank you,
Berni

training_image1.tif (1.3 MB)

Hi @Streptomyces003 we suffer the same issue for fungal hyphae, where filaments which cross eachother, suddenly become 1 larger object, when using classical image segmentatation, watershedding only breaks the filaments up into tiny bits.

I will be following this with huge interest!

Check out HyphaTracker https://www-nature-com.manchester.idm.oclc.org/articles/s41598-017-19103-1

Good luck!

Best wishes,

Darren

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