This page lists the jupyter notebooks (for downloading the data from public resource) and configuration files (for training and inference) for all experiments in our pre-print. These can also be used as examples for walking through different applications.
| Application | data preparation | training config | inference config |
|---|---|---|---|
| 3D labelfree prediction | notebook | FCN, pix2pix_from_scratch, pix2pix_transfer_learning | FCN, ix2pix |
| 2D labelfree prediction | notebook | FCN | FCN |
| 2D semantic segmentation | notebook | FCN | FCN |
| 3D semantic segmentation | notebook | FCN | FCN |
| 2D instance segmentation | notebook | EmbedSeg | Embedseg |
| 3D instance segmentation* | notebook | EmbedSeg_fluorescent_pretrain, EmbedSeg_fluoresenct_finetune, EmbedSeg_brightfield_pretrain, EmbedSeg_brightfield_finetune, EmbedSeg_FBL_pretrain, EmbedSeg_FBL_finetune | Embedseg_fluo, EmbedSeg_brightfield, EmbedSeg_FBL |
| 2D unsupervised segmentation | notebook | FCN_unpair | FCN |
| 3D unsupervised segmentation | notebook | FCN_unpair | FCN |
| 2D synthetic image generation | notebook | pix2pix | pix2pix |
| 3D synthetic image generation | notebook | pix2pix | pix2pix |
| image restoration / denoising | notebook | FCN | FCN |
| image modality transfer | notebook | FCN | FCN |
| staining transformation | notebook | pix2pix | pix2pix |