 }})
Plot particles by model outputs such as UMAP embeddings of z-latent-space axes.
Use lasso selection to write --ind .pkl files, or
load image caches to view images across particle selections.
 }})
Plot particles across a grid of squares, one for each combination of z-latent-space axes.
Choose color covariates from model outputs and dataset attributes as well as different clustering methods
to display on the diagonal of the plot grid.
 }})
Interactive 3D scatterplot of three z-latent-space axes, with optional color from model
outputs and dataset attributes.
Use the histogram or discrete toggles in the legend beside the plot to filter seen in plot.
 }})
3D scatter of vol-PCA embeddings generated by
analyze_landscape_full
for epoch {{ exp_epoch }}.
Use the histogram or discrete toggles in the legend beside the plot to filter particles, and create volume
trajectories and animations by selecting individual 3D points.
 }})
Explore k-means sketch volumes in PCA space from analyze_landscape for
epoch {{ exp_epoch }}, select volumes, preview GIFs (cycle or rotate), and save under
landscape.N/kmeansK/.
 }})
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.
Plot dataset particles by model outputs such as z-latent-space dimensions or analysis covariates such as UMAP
embeddings.
Use lasso selection to write --ind .pkl files.
Activate this interface by runningcryodrgn dashboard <outdir>.
Activate this interface by loading an output directory with single-particle image previews.
{% endif %}
Grid of scatters across latent dimensions and embeddings (PCA / UMAP on the diagonal when available).
Activate this interface by runningcryodrgn 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 runningcryodrgn dashboard <outdir>.
Activate this interface by loading a run with at least three latent dimensions (current: {{ zdim }}).
{% endif %}
Draw a line through the latent scatter to generate volumes along a trajectory — direct interpolation or nearest-neighbor mode — with ChimeraX previews.
{% if command_builder_only %}Activate this interface by runningcryodrgn dashboard <outdir>.
Activate this interface by running dashboard on a CUDA-enabled machine.
3D scatter in vol_pca_all.pkl space for z.sampled.pkl from
cryodrgn analyze_landscape_full, with colour from particle and
landscape covariates (scatter only).
Activate this interface by runningcryodrgn dashboard <outdir>
on
an outdir for whichcryodrgn analyze_landscape_full
has been run for at least one epoch.
Needs landscape.{{ exp_epoch }}/landscape_full/z.sampled.pkl,
ind.sampled.pkl, and vol_pca_all.pkl with at least three PCA columns. Run
cryodrgn analyze_landscape_full <outdir> {{ exp_epoch }} or switch epoch in the nav.
Explore k-means sketch volumes in PCA space from analyze_landscape, select volumes, preview GIFs
(cycle or rotate), and save under landscape.N/kmeansK/.
Activate this interface by runningcryodrgn dashboard <outdir>
on
an outdir for whichcryodrgn analyze_landscape
has been
run for at least one epoch.
No complete landscape output for epoch {{ exp_epoch }}
(landscape.{{ exp_epoch }} with vol_pca_* and matching kmeans*).
Run cryodrgn analyze_landscape <outdir> {{ exp_epoch }} or switch epoch in the nav.