pnnl/brain_ohsu
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Light sheet microscopy has made possible the 3D imaging of both fixed and live biological tissue, with samples as large as the entire mouse brain. We fine-tuned an existing model, TrailMap, using expert labeled data from axonal structures in neocortex. Without changing the network architecture, we implemented nnU-Net framework modifications in data augmentation, data foreground sampling, window learning rate, and the inference overlap method. The resulting model from these combined approaches yielded an improved F1 score
- Short Name / Acronym:
- brain_ohsu
- Site Accession Number:
- Battelle IPID 32777-E
- Software Type:
- Scientific
- License(s):
- BSD 2-clause "Simplified" License
- Research Organization:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
- Sponsoring Organization:
- USDOEPrimary Award/Contract Number:AC05-76RL01830
- DOE Contract Number:
- AC05-76RL01830
- Code ID:
- 114417
- OSTI ID:
- code-114417
- Country of Origin:
- United States
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