Build neural network, deep learning

I am attempting to annotate bacterial cell foci. They are easily observed by eye, but have varied intensities making it very difficult for microbeJ to distinguish them. I was wondering if there is a way to manually identify the foci to build a neural network. Any software suggestions would be very helpful. Thanks.

hi,

this should be easily possible. I can recommend the Fiji implementation here.

https://lmb.informatik.uni-freiburg.de/resources/opensource/unet/

this is fairly easy to install with basic linux knowledge.

alternatively you may want to build it in python look at this youtube channel here: https://www.youtube.com/channel/UC34rW-HtPJulxr5wp2Xa04w

either way you will need a cuda capable gpu. good luck

Thank you! I will give this a try.

https://www.nature.com/articles/s42003-019-0356-z

here is the relevant publication.

the hardest part for me was getting the correct driver with cuda 10 installed. If you have issues feel free to ask me but i cant guaratee that i can help.