3D segmentation and annotations

[pr4deepr]

A key feature that is requested is neuron segmentation in 3D.
It is possible, but as with any deep learning problem, generating a model requires manual annotation of data.
Challenges with 3D annotation:

• More effort annotating in 3D
• Variabiliity in image acquisition -> Anisotropic data ?.
• Image Quality: Variability in signal to noise ratio among images

The good news is that there is plenty of public data available now. Two main ones are:

• Mouse enteric neurons and subtypes: https://sparc.science/datasets/178/version/1
• Human enteric neurons and subtypes: https://sparc.science/datasets/55?type=dataset

This could be a community driven effort.. Perhaps make data available for annotation on a website. Apeer??

Once annotation is generated, it wouldn't be too challenging to generate a 3D segmentation model.