cryodrgn 2.2.0

cryoDRGN heterogeneous reconstruction

:snowflake::dragon: cryoDRGN: Deep Reconstructing Generative Networks for cryo-EM heterogeneous reconstruction

CryoDRGN is a neural network based algorithm for heterogeneous cryo-EM reconstruction. In particular, the method models a continuous distribution over 3D structures by using a neural network based representation for the volume.

Manuscripts:

CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks. Ellen D. Zhong, Tristan Bepler, Bonnie Berger*, Joseph H. Davis*. https://www.nature.com/articles/s41592-020-01049-4

Reconstructing continuous distributions of 3D protein structure from cryo-EM images. Ellen D. Zhong, Tristan Bepler, Joseph H. Davis*, Bonnie Berger*. ICLR 2020, Spotlight presentation, https://arxiv.org/abs/1909.05215

Documentation:

The latest documentation for cryoDRGN is available here. This includes an overview and walkthrough of cryoDRGN installation, training and analysis.

A more in-depth manuscript version of the tutorial is available here.

Old Documentation pages are available at notion.so.

A quick start is provided below.

Post any questions as an Github issue or to our google group: https://groups.google.com/g/cryodrgn.

New in Version 1.x

Version 1.1

Updated default parameters for cryodrgn train_vae with modified positional encoding, larger model architecture, and accelerated mixed-precision training turned on by default:

• Mixed precision training is now turned on by default (Use --no-amp to revert to single precision training)
• Encoder/decoder architecture is now 1024x3 by default (Use --enc-dim 256 and --dec-dim 256 to revert)
• Gaussian Fourier featurization for faster training and higher resolution density maps (Use --pe-type geom_lowf to revert)

Version 1.0

The official version 1.0 release. This version introduces several new tools for analysis of the reconstructed ensembles, and adds functionality for calling utility scripts with cryodrgn_utils <command>.

• NEW: cryodrgn analyze_landscape and cryodrgn analyze_landscape_full for automatic assignment of classes and conformational landscape visualization. Documentation for this new feature is here: https://www.notion.so/cryodrgn-conformational-landscape-analysis-a5af129288d54d1aa95388bdac48235a.
• NEW: Faster training and higher resolution model with Gaussian Fourier featurization (Use --pe-type gaussian)
• NEW: cryodrgn_utils <command> -h for standalone utility scripts
• NEW: cryodrgn_utils write_star for converting cryoDRGN particle selections to .star files
• Add pytorch native mixed precision training and fix support for pytorch 1.9+

Previous versions

Version 0.3.4

• FIX: Bug in write_starfile.py when provided particle stack is chunked (.txt file)
• Support micrograph coordinates and additional column headers to write_starfile.py
• New helper scripts: analyze_convergence.py (in beta testing) contributed by Barrett Powell (thanks!) and make_random_selection.py for splitting up particle stacks for training

Version 0.3.3

• Faster image preprocessing and smaller memory footprint
• New: cryodrgn preprocess for large datasets (in beta testing - see this Notion doc for details)
• Known issue with PyTorch version 1.9+

Version 0.3.2

• New: cryoDRGN_filtering.ipynb for interactive filtering/selection of images from the dataset
• New: cryodrgn view_config
• Minor performance improvements and compatibility fixes

Version 0.3.1

• New: Script write_starfile.py to convert (filtered) particle selection to a .star file
• More visualizations in cryodrgn analyze

Version 0.3.0

• New: GPU parallelization with flag --multigpu
• New: Mode for accelerated mixed precision training with flag --amp, available for NVIDIA tensor core GPUs
• Interface update:
  • Renamed encoder arguments --qdim and --qlayers to --enc-dim and --enc-layers
  • Renamed decoder arguments --pdim and --players to --dec-dim and --dec-layers
• Argument default changes:
  • Flipped the default for --invert-data to True by default
  • Flipped the default for --window to True by default
• Updated training recommendations in below quick start guide
• Updates to cryodrgn analyze
  • More visualizations
  • Order kmeans volumes according to distances in latent space (previously random)
  • More features for particle selection and filtering in the Jupiter notebook

Version 0.2.1

• New: Parsing of RELION 3.1 files
• Fix: Compatibility with pytorch 1.5

Version 0.2.0

• New interface and proper python packaging with setup.py. This version has identical functionality and argument usage as previous versions, however tools are now available from a common entry point. See:

  $ cryodrgn <command> -h

• New analysis pipeline cryodrgn analyze

• New latent space traversal scripts with cryodrgn graph_traversal and cryodrgn pc_traversal.

Installation/dependencies:

To install cryoDRGN, git clone the source code and install the following dependencies with anaconda:

# Create conda environment
conda create --name cryodrgn1 python=3.9
conda activate cryodrgn1

# Install dependencies
conda install pytorch -c pytorch
conda install pandas

# Install dependencies for latent space visualization
conda install seaborn scikit-learn
conda install umap-learn jupyterlab ipywidgets cufflinks-py "nodejs>=15.12.0" -c conda-forge
jupyter labextension install @jupyter-widgets/jupyterlab-manager --no-build
jupyter labextension install jupyterlab-plotly --no-build
jupyter labextension install plotlywidget --no-build
jupyter lab build

# Clone source code and install
git clone https://github.com/zhonge/cryodrgn.git
cd cryodrgn
pip install .

A detailed installation and testing guide is provided here: https://www.notion.so/cryoDRGN-installation-with-anaconda-4cff0367d9b241bb8d902efe339d01e6

Quickstart: heterogeneous reconstruction with consensus poses

1. Preprocess image stack

First resize your particle images using the cryodrgn downsample command:

$ cryodrgn downsample -h
usage: cryodrgn downsample [-h] -D D -o MRCS [--is-vol] [--chunk CHUNK]
                           [--datadir DATADIR]
                           mrcs

Downsample an image stack or volume by clipping fourier frequencies

positional arguments:
  mrcs               Input particles or volume (.mrc, .mrcs, .star, or .txt)

optional arguments:
  -h, --help         show this help message and exit
  -D D               New box size in pixels, must be even
  -o MRCS            Output projection stack (.mrcs)
  --is-vol           Flag if input .mrc is a volume
  --chunk CHUNK      Chunksize (in # of images) to split particle stack when
                     saving
  --relion31         Flag for relion3.1 star format
  --datadir DATADIR  Optionally provide path to input .mrcs if loading from a
                     .star or .cs file

Since larger images take (much) longer to train, we recommend first downsampling images to 128x128:

$ cryodrgn downsample [input particle stack] -D 128 -o particles.128.mrcs

The maximum recommended image size is D=256, so we also recommend downsampling your images to D=256 if your images are larger than 256x256:

$ cryodrgn downsample [input particle stack] -D 256 -o particles.256.mrcs

The input file format can be a single .mrcs file, a .txt file containing paths to multiple .mrcs files, a .star file, or a cryoSPARC .cs file. For the latter two options, if the relative paths to the .mrcs are broken, the argument --datadir can be used to supply the path to where the .mrcs files are located.

If there are memory issues with downsampling large particle stacks, add the --chunk 10000 argument to save images as separate .mrcs files of 10k images.

2. Parse image poses from a consensus homogeneous reconstruction

CryoDRGN expects image poses to be stored in a binary pickle format (.pkl). Use the parse_pose_star or parse_pose_csparc command to extract the poses from a .star file or a .cs file, respectively.

Example usage to parse image poses from a RELION 3.1 starfile:

$ cryodrgn parse_pose_star particles.star -o pose.pkl -D 300

Example usage to parse image poses from a cryoSPARC homogeneous refinement particles.cs file:

$ cryodrgn parse_pose_csparc cryosparc_P27_J3_005_particles.cs -o pose.pkl -D 300

The -D argument should be set to the box size of the original consensus reconstruction (before any downsampling).

Note: Poses should be obtained from a C1 consensus refinement! (See https://github.com/zhonge/cryodrgn/issues/21)

3. Parse CTF parameters from a .star/.cs file

CryoDRGN expects CTF parameters in be stored a binary pickle format (.pkl). Use the parse_ctf_star or parse_ctf_csparc command to extract the relevant CTF parameters from a .star file or a .cs file, respectively.

Example usage for a .star file:

$ cryodrgn parse_ctf_star particles.star -D 300 --Apix 1.03 -o ctf.pkl

The -D and --Apix arguments should be set to the box size and Angstrom/pixel of the original .mrcs file (before any downsampling).

Example usage for a .cs file:

$ cryodrgn parse_ctf_csparc cryosparc_P27_J3_005_particles.cs -o ctf.pkl

4. (Optional) Test pose/CTF parameters parsing

Next, test that pose and CTF parameters were parsed correctly using the voxel-based backprojection script. The goal is to quickly verify that there are no major problems with the extracted values and that the output structure resembles the structure from the consensus reconstruction before beginning training.

Example usage:

$ cryodrgn backproject_voxel projections.128.mrcs \
        --poses pose.pkl \
        --ctf ctf.pkl \
        -o backproject.128.mrc

The output structure backproject.128.mrc will not match the consensus reconstruction exactly as the backproject_voxel command backprojects phase-flipped particles onto the voxel grid, and by default only uses the first 10k images. If the structure is too noisy, you can increase the number of images that are used with the --first argument.

Note: If the volume does not resemble your structure, you may need to use the flag --uninvert-data. This flips the data sign (e.g. light-on-dark or dark-on-light), which may be needed depending on the convention used in upstream processing tools.

5. Running cryoDRGN heterogeneous reconstruction

When the input images (.mrcs), poses (.pkl), and CTF parameters (.pkl) have been prepared, a cryoDRGN model can be trained with following command:

$ cryodrgn train_vae -h

usage: cryodrgn train_vae [-h] -o OUTDIR --zdim ZDIM --poses POSES [--ctf pkl]
                          [--load WEIGHTS.PKL] [--checkpoint CHECKPOINT]
                          [--log-interval LOG_INTERVAL] [-v] [--seed SEED]
                          [--ind PKL] [--uninvert-data] [--no-window]
                          [--window-r WINDOW_R] [--datadir DATADIR] [--lazy]
                          [--preprocessed] [--max-threads MAX_THREADS]
                          [--tilt TILT] [--tilt-deg TILT_DEG] [-n NUM_EPOCHS]
                          [-b BATCH_SIZE] [--wd WD] [--lr LR] [--beta BETA]
                          [--beta-control BETA_CONTROL] [--norm NORM NORM]
                          [--no-amp] [--multigpu] [--do-pose-sgd]
                          [--pretrain PRETRAIN] [--emb-type {s2s2,quat}]
                          [--pose-lr POSE_LR] [--enc-layers QLAYERS]
                          [--enc-dim QDIM]
                          [--encode-mode {conv,resid,mlp,tilt}]
                          [--enc-mask ENC_MASK] [--use-real]
                          [--dec-layers PLAYERS] [--dec-dim PDIM]
                          [--pe-type {geom_ft,geom_full,geom_lowf,geom_nohighf,linear_lowf,gaussian,none}]
                          [--feat-sigma FEAT_SIGMA] [--pe-dim PE_DIM]
                          [--domain {hartley,fourier}]
                          [--activation {relu,leaky_relu}]
                          particles

Train a VAE for heterogeneous reconstruction with known pose

positional arguments:
  particles             Input particles (.mrcs, .star, .cs, or .txt)

optional arguments:
  -h, --help            show this help message and exit
  -o OUTDIR, --outdir OUTDIR
                        Output directory to save model
  --zdim ZDIM           Dimension of latent variable
  --poses POSES         Image poses (.pkl)
  --ctf pkl             CTF parameters (.pkl)
  --load WEIGHTS.PKL    Initialize training from a checkpoint
  --checkpoint CHECKPOINT
                        Checkpointing interval in N_EPOCHS (default: 1)
  --log-interval LOG_INTERVAL
                        Logging interval in N_IMGS (default: 1000)
  -v, --verbose         Increaes verbosity
  --seed SEED           Random seed

Dataset loading:
  --ind PKL             Filter particle stack by these indices
  --uninvert-data       Do not invert data sign
  --no-window           Turn off real space windowing of dataset
  --window-r WINDOW_R   Windowing radius (default: 0.85)
  --datadir DATADIR     Path prefix to particle stack if loading relative
                        paths from a .star or .cs file
  --lazy                Lazy loading if full dataset is too large to fit in
                        memory (Should copy dataset to SSD)
  --preprocessed        Skip preprocessing steps if input data is from
                        cryodrgn preprocess_mrcs
  --max-threads MAX_THREADS
                        Maximum number of CPU cores for FFT parallelization
                        (default: 16)

Tilt series:
  --tilt TILT           Particles (.mrcs)
  --tilt-deg TILT_DEG   X-axis tilt offset in degrees (default: 45)

Training parameters:
  -n NUM_EPOCHS, --num-epochs NUM_EPOCHS
                        Number of training epochs (default: 20)
  -b BATCH_SIZE, --batch-size BATCH_SIZE
                        Minibatch size (default: 8)
  --wd WD               Weight decay in Adam optimizer (default: 0)
  --lr LR               Learning rate in Adam optimizer (default: 0.0001)
  --beta BETA           Choice of beta schedule or a constant for KLD weight
                        (default: 1/zdim)
  --beta-control BETA_CONTROL
                        KL-Controlled VAE gamma. Beta is KL target. (default:
                        None)
  --norm NORM NORM      Data normalization as shift, 1/scale (default: 0, std
                        of dataset)
  --no-amp              Do not use mixed-precision training
  --multigpu            Parallelize training across all detected GPUs

Pose SGD:
  --do-pose-sgd         Refine poses with gradient descent
  --pretrain PRETRAIN   Number of epochs with fixed poses before pose SGD
                        (default: 1)
  --emb-type {s2s2,quat}
                        SO(3) embedding type for pose SGD (default: quat)
  --pose-lr POSE_LR     Learning rate for pose optimizer (default: 0.0003)

Encoder Network:
  --enc-layers QLAYERS  Number of hidden layers (default: 3)
  --enc-dim QDIM        Number of nodes in hidden layers (default: 1024)
  --encode-mode {conv,resid,mlp,tilt}
                        Type of encoder network (default: resid)
  --enc-mask ENC_MASK   Circular mask of image for encoder (default: D/2; -1
                        for no mask)
  --use-real            Use real space image for encoder (for convolutional
                        encoder)

Decoder Network:
  --dec-layers PLAYERS  Number of hidden layers (default: 3)
  --dec-dim PDIM        Number of nodes in hidden layers (default: 1024)
  --pe-type {geom_ft,geom_full,geom_lowf,geom_nohighf,linear_lowf,gaussian,none}
                        Type of positional encoding (default: gaussian)
  --feat-sigma FEAT_SIGMA
                        Scale for random Gaussian features
  --pe-dim PE_DIM       Num features in positional encoding (default: image D)
  --domain {hartley,fourier}
                        Decoder representation domain (default: fourier)
  --activation {relu,leaky_relu}
                        Activation (default: relu)

Many of the parameters of this script have sensible defaults. The required arguments are:

• an input image stack (.mrcs or other listed file types)
• --poses, image poses (.pkl) that correspond to the input images
• --ctf, ctf parameters (.pkl), unless phase-flipped images are used
• --zdim, the dimension of the latent variable
• -o, a clean output directory for storing results

Additional parameters which are typically set include:

• -n, Number of epochs to train
• --uninvert-data, Use if particles are dark on light (negative stain format)
• Architecture parameters with --enc-layers, --enc-dim, --dec-layers, --dec-dim
• --multigpu to enable parallelized training across multiple GPUs

Recommended usage:

1. It is highly recommended to first train on lower resolution images (e.g. D=128) to sanity check results and perform any particle filtering.

Example command to train a cryoDRGN model for 25 epochs on an image dataset projections.128.mrcs with poses pose.pkl and ctf parameters ctf.pkl:

# 8-D latent variable model, small images
$ cryodrgn train_vae projections.128.mrcs \
        --poses pose.pkl \
        --ctf ctf.pkl \
        --zdim 8 -n 25 \
        -o 00_cryodrgn128

2. After validation, pose optimization, and any necessary particle filtering, then train on the full resolution images (up to D=256):

Example command to train a cryoDRGN model for 25 epochs on an image dataset projections.256.mrcs with poses pose.pkl and ctf parameters ctf.pkl:

# 8-D latent variable model, larger images
$ cryodrgn train_vae projections.256.mrcs \
        --poses pose.pkl \
        --ctf ctf.pkl \
        --zdim 8 -n 25 \
        -o 01_cryodrgn256

The number of epochs -n refers to the number of full passes through the dataset for training, and should be modified depending on the number of particles in the dataset. For a 100k particle dataset on 1 V100 GPU, the above settings required ~12 min/epoch for D=128 images and ~47 min/epoch for D=256 images.

If you would like to train longer, a training job can be extended with the --load argument. For example to extend the training of the previous example to 50 epochs:

$ cryodrgn train_vae projections.256.mrcs \
        --poses pose.pkl \
        --ctf ctf.pkl \
        --zdim 8 -n 50 \
        -o 01_cryodrgn256 \
        --load 01_cryodrgn256/weights.24.pkl # 0-based indexing

Accelerated training with GPU parallelization

Use cryoDRGN's --multigpu flag to enable parallelized training across all detected GPUs on the machine. To select specific GPUs for cryoDRGN to run on, use the environmental variable CUDA_VISIBLE_DEVICES, e.g.:

$ cryodrgn train_vae ... # Run on GPU 0
$ cryodrgn train_vae ... --multigpu # Run on all GPUs on the machine
$ CUDA_VISIBLE_DEVICES=0,3 cryodrgn train_vae ... --multigpu # Run on GPU 0,3

When training is parallelized across multiple GPUs, the batch size (number of images trained in each mini-batch of SGD; default -b 8) will be automatically scaled by the number of available GPUs to better take advantage of parallelization. Depending on your compute resources, GPU utilization may be improved with -b 16. However, note that GPU parallelization, while leading to a faster wall-clock time per epoch, may require increasing the total number of epochs, since the training dynamics are affected (fewer model updates per epoch with larger -b).

Note: We recommend using --multigpu for large images, e.g. D=256. GPU computation may not be the training bottleneck for smaller images (D=128). In this case, GPU parallelization may have a limited effect on the wall clock training time (while taking up additional compute resources).

Local pose refinement -- EXPERIMENTAL!

Depending on the quality of the consensus reconstruction, image poses may contain errors. Image poses may be locally refined using the --do-pose-sgd flag. Please consult Ellen Zhong ([e-mail]) for details.

6. Analysis of results

Once the model has finished training, the output directory will contain a configuration file config.pkl, neural network weights weights.pkl, image poses (if performing pose sgd) pose.pkl, and the latent embeddings for each image z.pkl. The latent embeddings are provided in the same order as the input particles. To analyze these results, use the cryodrgn analyze command to visualize the latent space and generate structures. cryodrgn analyze will also provide a template jupyter notebook for further interactive visualization and analysis.

NEW in version 1.0: There are two additional tools cryodrgn analyze_landscape and cryodrgn analyze_landscape_full for more comprehensive and auomated analyses of cryodrgn results.

cryodrgn analyze

$ cryodrgn analyze -h
usage: cryodrgn analyze [-h] [--device DEVICE] [-o OUTDIR] [--skip-vol]
                        [--skip-umap] [--Apix APIX] [--flip] [--invert]
                        [-d DOWNSAMPLE] [--pc PC] [--ksample KSAMPLE]
                        workdir epoch

Visualize latent space and generate volumes

positional arguments:
  workdir               Directory with cryoDRGN results
  epoch                 Epoch number N to analyze (0-based indexing,
                        corresponding to z.N.pkl, weights.N.pkl)

optional arguments:
  -h, --help            show this help message and exit
  --device DEVICE       Optionally specify CUDA device
  -o OUTDIR, --outdir OUTDIR
                        Output directory for analysis results (default:
                        [workdir]/analyze.[epoch])
  --skip-vol            Skip generation of volumes
  --skip-umap           Skip running UMAP

Extra arguments for volume generation:
  --Apix APIX           Pixel size to add to .mrc header (default: 1 A/pix)
  --flip                Flip handedness of output volumes
  --invert              Invert contrast of output volumes
  -d DOWNSAMPLE, --downsample DOWNSAMPLE
                        Downsample volumes to this box size (pixels)
  --pc PC               Number of principal component traversals to generate
                        (default: 2)
  --ksample KSAMPLE     Number of kmeans samples to generate (default: 20)

This script runs a series of standard analyses:

• PCA visualization of the latent embeddings
• UMAP visualization of the latent embeddings
• Generation of volumes. See note [1].
• Generation of trajectories along the first and second principal components of the latent embeddings
• Generation of a template jupyter notebook that may be used for further interactive analyses, visualization, and volume generation
• Generation of a template jupyter notebook for particle filtering and selection

Example usage to analyze results from the direction 01_cryodrgn256 containing results after 25 epochs of training:

$ cryodrgn analyze 01_cryodrgn256 24 --Apix 1.31

Notes:

[1] Volumes are generated after k-means clustering of the latent embeddings with k=20 by default. Note that we use k-means clustering here not to identify clusters, but to segment the latent space and generate structures from different regions of the latent space. The number of structures that are generated may be increased with the option --ksample.

[2] The cryodrgn analyze command chains together a series of calls to cryodrgn eval_vol and scripts that can be run separately for more flexibility. These scripts are located in the analysis_scripts directory within the source code.

Generating additional volumes

Additional structures may be generated using cryodrgn eval_vol:

$ cryodrgn eval_vol -h
usage: cryodrgn eval_vol [-h] -c PKL -o O [--prefix PREFIX] [-v]
                         [-z [Z [Z ...]]] [--z-start [Z_START [Z_START ...]]]
                         [--z-end [Z_END [Z_END ...]]] [-n N] [--zfile ZFILE]
                         [--Apix APIX] [--flip] [-d DOWNSAMPLE]
                         [--norm NORM NORM] [-D D] [--enc-layers QLAYERS]
                         [--enc-dim QDIM] [--zdim ZDIM]
                         [--encode-mode {conv,resid,mlp,tilt}]
                         [--dec-layers PLAYERS] [--dec-dim PDIM]
                         [--enc-mask ENC_MASK]
                         [--pe-type {geom_ft,geom_full,geom_lowf,geom_nohighf,linear_lowf,none}]
                         [--pe-dim PE_DIM] [--domain {hartley,fourier}]
                         [--l-extent L_EXTENT]
                         [--activation {relu,leaky_relu}]
                         weights

Evaluate the decoder at specified values of z

positional arguments:
  weights               Model weights

optional arguments:
  -h, --help            show this help message and exit
  -c PKL, --config PKL  CryoDRGN config.pkl file
  -o O                  Output .mrc or directory
  --prefix PREFIX       Prefix when writing out multiple .mrc files (default:
                        vol_)
  -v, --verbose         Increaes verbosity

Specify z values:
  -z [Z [Z ...]]        Specify one z-value
  --z-start [Z_START [Z_START ...]]
                        Specify a starting z-value
  --z-end [Z_END [Z_END ...]]
                        Specify an ending z-value
  -n N                  Number of structures between [z_start, z_end]
  --zfile ZFILE         Text file with z-values to evaluate

Volume arguments:
  --Apix APIX           Pixel size to add to .mrc header (default: 1 A/pix)
  --flip                Flip handedness of output volume
  -d DOWNSAMPLE, --downsample DOWNSAMPLE
                        Downsample volumes to this box size (pixels)

Overwrite architecture hyperparameters in config.pkl:
  --norm NORM NORM
  -D D                  Box size
  --enc-layers QLAYERS  Number of hidden layers
  --enc-dim QDIM        Number of nodes in hidden layers
  --zdim ZDIM           Dimension of latent variable
  --encode-mode {conv,resid,mlp,tilt}
                        Type of encoder network
  --dec-layers PLAYERS  Number of hidden layers
  --dec-dim PDIM        Number of nodes in hidden layers
  --enc-mask ENC_MASK   Circular mask radius for image encoder
  --pe-type {geom_ft,geom_full,geom_lowf,geom_nohighf,linear_lowf,none}
                        Type of positional encoding
  --pe-dim PE_DIM       Num sinusoid features in positional encoding (default:
                        D/2)
  --domain {hartley,fourier}
  --l-extent L_EXTENT   Coordinate lattice size
  --activation {relu,leaky_relu}
                        Activation (default: relu)

Example usage:

To generate a volume at a single value of the latent variable:

$ cryodrgn eval_vol [YOUR_WORKDIR]/weights.pkl --config [YOUR_WORKDIR]/config.pkl -z ZVALUE -o reconstruct.mrc

The number of inputs for -z must match the dimension of your latent variable.

Or to generate a trajectory of structures from a defined start and ending point, use the --z-start and --z-end arugments:

$ cryodrgn eval_vol [YOUR_WORKDIR]/weights.pkl --config [YOUR_WORKDIR]/config.pkl --z-start -3 --z-end 3 -n 20 -o [WORKDIR]/trajectory

This example generates 20 structures at evenly spaced values between z=[-3,3], assuming a 1-dimensional latent variable model.

Finally, a series of structures can be generated using values of z given in a file specified by the arugment --zfile:

$ cryodrgn eval_vol [WORKDIR]/weights.pkl --config [WORKDIR]/config.pkl --zfile zvalues.txt -o [WORKDIR]/trajectory

The input to --zfile is expected to be an array of dimension (N_volumes x zdim), loaded with np.loadtxt.

Making trajectories

Two additional commands can be used in conjunction with cryodrgn eval_vol to generate trajectories:

$ cryodrgn pc_traversal -h
$ cryodrgn graph_traversal -h

These scripts produce a text file of z values that can be input to cryodrgn eval_vol to generate a series of structures that can be visualized as a trajectory in ChimeraX (https://www.cgl.ucsf.edu/chimerax).

An example usage of the graph traversal algorithm is here (https://github.com/zhonge/cryodrgn/issues/16#issuecomment-668897007).

CryoDRGN2 -- Ab Initio Reconstruction

To perform ab initio heterogeneous reconstruction, use cryodrgn abinit_het. The arguments are similar to cryodrgn train_vae, but the --poses argument is not required.

For homogeneous reconstruction, run cryodrgn abinit_homo.

Documentation: https://www.notion.so/CryoDRGN2-quickstart-322823599fce4bd7a391d00bf749ab1f.

The defaults match the settings reported in the CryoDRGN2 manuscript.

usage: cryodrgn abinit_het [-h] -o OUTDIR --zdim ZDIM [--ctf pkl]
                           [--load LOAD] [--load-poses LOAD_POSES]
                           [--checkpoint CHECKPOINT]
                           [--log-interval LOG_INTERVAL] [-v] [--seed SEED]
                           [--ind PKL] [--uninvert-data] [--no-window]
                           [--window-r WINDOW_R] [--datadir DATADIR]
                           [--lazy-single] [--lazy] [--preprocessed]
                           [--max-threads MAX_THREADS] [--tilt TILT]
                           [--tilt-deg TILT_DEG] [--enc-only] [-n NUM_EPOCHS]
                           [-b BATCH_SIZE] [--wd WD] [--lr LR] [--beta BETA]
                           [--beta-control BETA_CONTROL]
                           [--equivariance EQUIVARIANCE]
                           [--eq-start-it EQ_START_IT] [--eq-end-it EQ_END_IT]
                           [--norm NORM NORM] [--l-ramp-epochs L_RAMP_EPOCHS]
                           [--l-ramp-model L_RAMP_MODEL]
                           [--reset-model-every RESET_MODEL_EVERY]
                           [--reset-optim-every RESET_OPTIM_EVERY]
                           [--reset-optim-after-pretrain RESET_OPTIM_AFTER_PRETRAIN]
                           [--l-start L_START] [--l-end L_END] [--niter NITER]
                           [--t-extent T_EXTENT] [--t-ngrid T_NGRID]
                           [--t-xshift T_XSHIFT] [--t-yshift T_YSHIFT]
                           [--pretrain PRETRAIN] [--ps-freq PS_FREQ]
                           [--nkeptposes NKEPTPOSES]
                           [--base-healpy BASE_HEALPY]
                           [--pose-model-update-freq POSE_MODEL_UPDATE_FREQ]
                           [--enc-layers QLAYERS] [--enc-dim QDIM]
                           [--encode-mode {conv,resid,mlp,tilt}]
                           [--enc-mask ENC_MASK] [--use-real]
                           [--dec-layers PLAYERS] [--dec-dim PDIM]
                           [--pe-type {geom_ft,geom_full,geom_lowf,geom_nohighf,linear_lowf,gaussian,none}]
                           [--feat-sigma FEAT_SIGMA] [--pe-dim PE_DIM]
                           [--domain {hartley,fourier}]
                           [--activation {relu,leaky_relu}]
                           particles

Heterogeneous NN reconstruction with hierarchical pose optimization

positional arguments:
  particles             Input particles (.mrcs, .txt or .star)

optional arguments:
  -h, --help            show this help message and exit
  -o OUTDIR, --outdir OUTDIR
                        Output directory to save model
  --zdim ZDIM           Dimension of latent variable
  --ctf pkl             CTF parameters (.pkl)
  --load LOAD           Initialize training from a checkpoint
  --load-poses LOAD_POSES
                        Initialize training from a checkpoint
  --checkpoint CHECKPOINT
                        Checkpointing interval in N_EPOCHS (default: 1)
  --log-interval LOG_INTERVAL
                        Logging interval in N_IMGS (default: 1000)
  -v, --verbose         Increaes verbosity
  --seed SEED           Random seed

Dataset loading:
  --ind PKL             Filter particle stack by these indices
  --uninvert-data       Do not invert data sign
  --no-window           Turn off real space windowing of dataset
  --window-r WINDOW_R   Windowing radius (default: 0.85)
  --datadir DATADIR     Path prefix to particle stack if loading relative
                        paths from a .star or .cs file
  --lazy-single         Lazy loading if full dataset is too large to fit in
                        memory
  --lazy                Memory efficient training by loading data in chunks
  --preprocessed        Skip preprocessing steps if input data is from
                        cryodrgn preprocess_mrcs
  --max-threads MAX_THREADS
                        Maximum number of CPU cores for FFT parallelization
                        (default: 16)

Tilt series:
  --tilt TILT           Particle stack file (.mrcs)
  --tilt-deg TILT_DEG   X-axis tilt offset in degrees (default: 45)
  --enc-only            Use the tilt pair only in VAE and not in BNB search

Training parameters:
  -n NUM_EPOCHS, --num-epochs NUM_EPOCHS
                        Number of training epochs (default: 30)
  -b BATCH_SIZE, --batch-size BATCH_SIZE
                        Minibatch size (default: 8)
  --wd WD               Weight decay in Adam optimizer (default: 0)
  --lr LR               Learning rate in Adam optimizer (default: 0.0001)
  --beta BETA           Choice of beta schedule or a constant for KLD weight
                        (default: 1.0)
  --beta-control BETA_CONTROL
                        KL-Controlled VAE gamma. Beta is KL target. (default:
                        None)
  --equivariance EQUIVARIANCE
                        Strength of equivariance loss (default: None)
  --eq-start-it EQ_START_IT
                        It at which equivariance turned on (default: 100000)
  --eq-end-it EQ_END_IT
                        It at which equivariance max (default: 200000)
  --norm NORM NORM      Data normalization as shift, 1/scale (default: mean,
                        std of dataset)
  --l-ramp-epochs L_RAMP_EPOCHS
                        default: 0
  --l-ramp-model L_RAMP_MODEL
                        If 1, then during ramp only train the model up to
                        l-max
  --reset-model-every RESET_MODEL_EVERY
                        If set, reset the model every N epochs
  --reset-optim-every RESET_OPTIM_EVERY
                        If set, reset the optimizer every N epochs
  --reset-optim-after-pretrain RESET_OPTIM_AFTER_PRETRAIN
                        If set, reset the optimizer every N epochs

Pose Search parameters:
  --l-start L_START     Starting L radius (default: 12)
  --l-end L_END         End L radius (default: 32)
  --niter NITER         Number of iterations of grid subdivision
  --t-extent T_EXTENT   +/- pixels to search over translations (default: 10)
  --t-ngrid T_NGRID     Initial grid size for translations
  --t-xshift T_XSHIFT
  --t-yshift T_YSHIFT
  --pretrain PRETRAIN   Number of initial iterations with random poses
                        (default: 10000)
  --ps-freq PS_FREQ     Frequency of pose inference (default: every 5 epochs)
  --nkeptposes NKEPTPOSES
                        Number of poses to keep at each refinement interation
                        during branch and bound
  --base-healpy BASE_HEALPY
                        Base healpy grid for pose search. Higher means
                        exponentially higher resolution.
  --pose-model-update-freq POSE_MODEL_UPDATE_FREQ
                        If set, only update the model used for pose search
                        every N examples.

Encoder Network:
  --enc-layers QLAYERS  Number of hidden layers (default: 3)
  --enc-dim QDIM        Number of nodes in hidden layers (default: 256)
  --encode-mode {conv,resid,mlp,tilt}
                        Type of encoder network (default: resid)
  --enc-mask ENC_MASK   Circular mask of image for encoder (default: D/2; -1
                        for no mask)
  --use-real            Use real space image for encoder (for convolutional
                        encoder)

Decoder Network:
  --dec-layers PLAYERS  Number of hidden layers (default: 3)
  --dec-dim PDIM        Number of nodes in hidden layers (default: 256)
  --pe-type {geom_ft,geom_full,geom_lowf,geom_nohighf,linear_lowf,gaussian,none}
                        Type of positional encoding (default: gaussian)
  --feat-sigma FEAT_SIGMA
                        Scale for random Gaussian features (default: 0.5)
  --pe-dim PE_DIM       Num features in positional encoding (default: image D)
  --domain {hartley,fourier}
                        Decoder representation domain (default: fourier)
  --activation {relu,leaky_relu}
                        Activation (default: relu)

Contact

Please submit any bug reports, feature requests, or general usage feedback as a github issue, or post in the Google Group: https://groups.google.com/g/cryodrgn.