BoxNet is a deep residual convolutional network for particle picking and dirt masking in cryo-EM data. It's pre-trained on a lot of data and performs rather well.
The easiest way to use it is inside Warp. We are constantly re-training the model on the latest version of the training dataset. To benefit from that, grab the latest model from http://boxnet.warpem.com/models. Models containing a "Mask" suffix are pre-trained to also mask out dirt in micrographs. In case this leads to bad results, try a model without masking.
The training dataset is too large to fit in this repository. It is hosted at http://boxnet.warpem.com/trainingdata. The .zip file contains the entire corpus. To use it to re-train the model in Warp, put as many of the TIFF files as you want into the "boxnet2training" folder of your Warp installation.
To submit more data to the training repository, please use this page.
BoxNet can't pick helical filaments yet. We are especially looking for good examples of helical data to implement this feature!
| Access code | Sample | Synthetic | Carbon support | VPP | Released |
|---|---|---|---|---|---|
| EMPIAR-10017 | beta-galactosidase | ✓ | |||
| EMPIAR-10077 | 80S ribosome | ✓ | ✓ | ||
| EMPIAR-10078 | 20S proteasome | ✓ | ✓ | ||
| EMPIAR-10081 | HCN1 channel | ✓ | |||
| EMPIAR-10084 | Haemoglobin | ✓ | ✓ | ||
| EMPIAR-10089 | TcdA1 in prepore state | ✓ | |||
| EMPIAR-10097 | Influenza Hemagglutinin | ✓ | |||
| EMPIAR-10122 | Apoferritin | ✓ | ✓ | ||
| EMPIAR-10153 | 80S ribosome | ✓ | ✓ | ✓ | |
| EMPIAR-10156 | 80S ribosome | ✓ | ✓ | ||
| PDB-1sa0 | Tubulin-Colchicine | ✓ | ✓ | ||
| PDB-2gtl | Lumbricus Erythrocruorin | ✓ | ✓ | ||
| PDB-2wri | 70S ribosome | ✓ | ✓ | ||
| PDB-3j9i | 20S proteasome | ✓ | ✓ | ||
| PDB-4hhb | Haemoglobin | ✓ | ✓ | ||
| PDB-4zor | S37P MS2 viral capsid | ✓ | ✓ | ||
| PDB-5foj | Grapevine Fanleaf virus | ✓ | ✓ | ||
| PDB-5mmi | Chloroplast ribosome, large subunit | ✓ | ✓ | ||
| PDB-5ngm | 70S ribosome | ✓ | ✓ | ||
| PDB-5vy5 | Aldolase | ✓ | ✓ | ||
| PDB-5w3l | Rhi virus B14 | ✓ | ✓ | ||
| PDB-5w3s | TRPML3 channel | ✓ | ✓ | ||
| PDB-5xnl | Stacked PSII-LHCII supercomplex | ✓ | ✓ | ||
| PDB-5xwy | LbuCas13a-crRNA complex | ✓ | ✓ | ||
| PDB-5y6p | Phycobilisome | ✓ | ✓ | ||
| PDB-6az1 | 80S ribosome, small subunit | ✓ | ✓ | ||
| PDB-6b7n | Coronavirus spike protein | ✓ | ✓ | ||
| PDB-6b44 | CRISPR Csy surveillance complex | ✓ | ✓ | ||
| PDB-6bco | TRPM4 channel | ✓ | ✓ | ||
| PDB-6bcx | mTORC1 | ✓ | ✓ | ||
| PDB-6bhu | MRP1 | ✓ | ✓ | ||
| RNA Polymerase II complex | ✓ | ||||
| RNA Polymerase II complex | ✓ | ✓ | |||
| RNA Polymerase II complex | ✓ | ||||
| viral polymerase | ✓ | ||||
| nucleosome complex |
BoxNet is being developed by Dimitry Tegunov (tegunov@gmail.com) in Patrick Cramer's lab at the Max Planck Institute for Biophysical Chemistry in Göttingen, Germany.