CePNEM model analysis data and ANTSUN and microscopy neural network weights

Citation and Publication To cite this project (datasets, encoding data, methods, modeling, code, website, etc.), please refer to Atanas & Kim et al., 2023 below. Please cite the paper directly and DO NOT cite this repository. Brain-wide representations of behavior spanning multiple timescales and states in C. elegans Adam A. Atanas*, Jungsoo Kim*, Ziyu Wang, Eric Bueno, McCoy Becker, Di Kang, Jungyeon Park, Talya S. Kramer, Flossie K. Wan, Saba Baskoylu, Ugur Dag, Elpiniki Kalogeropoulou, Matthew A. Gomes, Cassi Estrem, Netta Cohen, Vikash K. Mansinghka, Steven W. Flavell * equal Contribution Links: https://doi.org/10.1016/j.cell.2023.07.035 https://pubmed.ncbi.nlm.nih.gov/37607537/ WormWideWeb Datasets in this project can be interactively visualized on: https://wormwideweb.org/ Features include: Find specific neurons Find specific datasets Contents 1. deepnet-weights.tar.bz2 contains the trained weights of the neural networks used in this project. 3dunet_540nm_voxels: 3D U-Net for segmenting neurons head_detector_unet: finding worm head landmark used in ANTSUN registration head_detector_unet_0622: an alternative version of the above, optimal for NeuroPAL datasets microscope_tracker: detecting keypoints for online tracking on the microscope behavior_nir: segmentation of the recorded NIR behavior images for behavior quantification 2. data files ANTSUN processed datasets and CePNEM processed model fits and analysis data. Check the project packages and notebooks in the project github repository (https://github.com/flavell-lab/AtanasKim-Cell2023/) on using these datasets. To get all behavior-neural datasets, please see processed_h5.tar.bz2