preprocessing and training scripts

axondeepseg / model_seg_nerve

Nerve area segmentation for axon density estimation in BF images

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preprocessing and training scripts #2

Closed hermancollin closed 7 months ago

hermancollin commented 9 months ago

Preprocessing, training and inference scripts should be put in a nnunet_scripts folder. @carlosnazzarian can you confirm you have access to this repo? e.g. assign yourself to this issue

List of things to add:

[x] script to convert data to nnunet format (see example here)
[x] setup_nnunet (for env vars)
[x] training script
[x] inference script (probably this one: run_inference.py)

carlosnazzarian commented 9 months ago

@hermancollin i confirm that i have access to this repository