Mouse Embryo Multi-Organ Segmentations (MEMOS): A 3D Slicer extension for automated segmentation of fetal mice using deep-learning. For details on the method please see the open-access paper in Biology Open . Step-by-step installation and use instructions, and detailed installation and usage instructions can be found as a supplementary file accompanying the paper.
Briefly you need:
- Install the MEMOs extension. As part of the installation, PyTorch extension will also be installed. Restart Slicer for changes to take effect.
- Switch to pytorch module and choose automatic install (one-time only. You can skip this, if you already installed PyTorch before)
- Switch to MEMOS module.
- MEMOS will automatically download the pretrained network (one-time). If it fails for any reason, you can manually download the pretrained network from this link.
- Obtain a sample dataset Eg. sample from IMPC
If you use this work, please cite Rolfe SM, Whikehart SM, Maga AM (2023) Deep learning enabled multi-organ segmentation of mouse embryos. Biology Open, 12(2):bio059698. https://doi.org/10.1242/bio.059698
This work was partly supported by grants NIH/OD032627 and NIH/HD104435.
