MEMOS

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:

1. Install the MEMOs extension. As part of the installation, PyTorch extension will also be installed. Restart Slicer for changes to take effect.
2. Switch to pytorch module and choose automatic install (one-time only. You can skip this, if you already installed PyTorch before)
3. Switch to MEMOS module.
4. 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.
5. 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

Funding

This work was partly supported by grants NIH/OD032627 and NIH/HD104435.