The notebook ANTSUN_2U.ipynb performs unsupservised NeuroPAL neuron labeling. It takes as input a fully-trained CellDiscoveryNet and a directory containing 4-D multispectral images of worms, their ROI (segmentation) images, and Euler-registered versions for every pair of images.
See the base ANTSUN pacakge for installation instructions.
This code assumes you have already run the make_CellDiscoveryNet_input.ipynb notebook and trained CellDiscoveryNet.
If you are using this code, please cite the following article:
Adam A. Atanas, Alicia Kun-Yang Lu, Jungsoo Kim, Saba Baskoylu, Di Kang, Talya S. Kramer, Eric Bueno, Flossie K. Wan, Steven W. Flavell
bioRxiv 2024; doi: https://doi.org/10.1101/2024.07.18.601886