kirkegaardlab/diffusionsplit

Diffusion Splitting for Instance Segmentation

Paper: https://www.biorxiv.org/content/10.1101/2023.07.07.548066v1

Installation

pip install -r requirements.txt
pip install https://github.com/zsef123/Connected_components_PyTorch/archive/refs/heads/main.zip

Dataset

Overlapping dataset can be downloaded at github.com/juliusbierk/cellpose-overlap.

Training

python split.py --data data/overlapdataset --model overlapdataset --train-all

download pretrained:

mkdir models
mkdir models/overlapdataset
cd models/overlapdataset
wget https://sid.erda.dk/share_redirect/AvuJczAyUI -O overlap_trained.zip
unzip overlap_trained.zip

Evaluation

python split.py --data data/overlapdataset --model overlapdataset --eval