morganfuture / boxnet

BoxNet implemented in TensorFlow and all current training data

BoxNet

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!

Current list of samples

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

Authorship

BoxNet is being developed by Dimitry Tegunov ([email protected]) in Patrick Cramer's lab at the Max Planck Institute for Biophysical Chemistry in Göttingen, Germany.