$ cryodrgn downsample -h$ cryodrgn train_vae -h$ cryodrgn analyze -h$ cryodrgn eval_vol -h{{ a.cli[0] }}\n \n {% elif a.w == 'number' %}\n \n \n {% else %}\n \n \n {% endif %}\n{% endmacro %}\n{% macro render_dataset_fieldset(cmd_key, datadir_id) %}\n {% set ds = (command_builder_schema[cmd_key] | selectattr('title', 'equalto', 'Dataset loading') | list | first) %}\n \n{% endmacro %}\n\n Pick a primary reconstruction command. The line below lists required arguments plus options you actually set (empty fields and CLI defaults are omitted).\n
\ncryodrgn abinit …\n
This page does not run training — copy the line into your shell or job script.
\n \nPlot dataset particles by model outputs such as z-latent-space dimensions or analysis covariates such as UMAP embeddings.
\n Use lasso selection to write --ind .pkl files,\n and optionally view dataset images or volume reconstructions for each particle.
Grid of scatters across latent dimensions and embeddings (PCA / UMAP on the diagonal when available).
\n \n {% endif %}\n {% if latent3d_active %}\n \nInteractive 3D scatter of three latent axes, with optional color from analysis columns when you have at least three z dimensions.
Compose a cryodrgn command you can copy and paste for tools such as abinit and train_vae — required args plus only the options you fill in.
Draw a line through the latent scatter to generate volumes along a trajectory — direct interpolation or nearest-neighbor mode — with ChimeraX previews.
\n \n {% endif %}\n\n {# Inactive interfaces start on next row #}\n {% if any_inactive %}\n \n {% endif %}\n\n {% if not explorer_active %}\nPlot dataset particles by model outputs such as z-latent-space dimensions or analysis covariates such as UMAP embeddings.
\n Use lasso selection to write --ind .pkl files.\n {% if command_builder_only %}\n
Activate this interface by running cryodrgn dashboard <outdir>.
Activate this interface by loading an output directory with single-particle image previews.
\n {% endif %}\nGrid of scatters across latent dimensions and embeddings (PCA / UMAP on the diagonal when available).
\nActivate this interface by running cryodrgn dashboard <outdir>.
Interactive 3D scatter of three latent axes, with optional color from analysis columns when you have at least three z dimensions.
Activate this interface by running cryodrgn dashboard <outdir>.
Activate this interface by loading a run with at least three latent dimensions (current: {{ zdim }}).
\n {% endif %}\nDraw a line through the latent scatter to generate volumes along a trajectory — direct interpolation or nearest-neighbor mode — with ChimeraX previews.
\n {% if command_builder_only %}\nActivate this interface by running cryodrgn dashboard <outdir>.
Activate this interface by using a CUDA-enabled machine and loading a run with model weights for the selected epoch.
\n {% endif %}\nEach point is a particle in the space of three latent coordinates you choose. Optional color encodes another quantity from the analysis table.
\n{{ reason }}
\nEach panel compares two latent coordinates. The diagonal shows a 2D embedding; one triangle colors particles by a covariate; the other shows a light scatter or density pattern.
\n\n \n
\n \nThe pairwise grid needs at least two latent coordinates. This reconstruction has {{ n }}.
\n{% elif kind == \"z3\" %}\nThe 3-D Latent Space Visualizer needs at least three latent coordinates. This reconstruction has {{ n }}.
\n{% elif kind == \"pca\" %}\nThe diagonal embedding needs PCA components in the analysis table for this epoch.
\n{% else %}\nThere is no numeric column available to color the lower panels.
\n{% endif %}\nChoose covariates for plot axes and point coloring. Use lasso selection to create a particle filtering index; generate images and volumes with or without a selection using the interface on the right.
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