This repository contains the implementation of the segmentation pipeline for SCNEM dataset
SCNEM is a ssEM dataset, consisting of an entire unilateral mouse SCN (suprachiasmatic nucleus) with dimensions of 384 μm × 704 μm × 273 μm. Raw data and multiscale reconstructions will be available upon publication.
The inference pipeline is developed based on PyTC and cloudvolume.
python main_inference.py --config-file /path/config.yaml --checkpoint /path/checkpoint.pth.tar