model_seg_unmyelinated_tem

Model for unmyelinated axon segmentation in TEM images, based on nnUNetv2.

Model overview

TODO image and description

Usage

To use the checkpoints provided in this repository, please see this temporary solution: https:/axondeepseg/nn-axondeepseg.

Data

The datasets can be found in the NeuroPoly internal data server. Look for datasets/data_axondeepseg_sickkids and data_axondeepseg_stanford.

TODO show how to use script to preprocess data

Training

For more detailed information on the training pipelines, see the sickkids_pipeline and stanford_pipeline folders.