Grid Visualization
CryoNAV provides multiple visualization modes for navigating datasets at different scales.
Grid atlas view
The low-magnification atlas image provides an overview of the entire grid, showing ice distribution and grid bar positions, with search map locations indicated on the atlas for spatial context.
Search map overlay
At the search map level, tilt series thumbnails are overlaid on the search map image at their acquisition coordinates, providing immediate spatial context: researchers can see at a glance which regions of a grid square yielded high-quality data and which suffered from thick ice or proximity to grid bars. The overlay is constructed automatically from stage coordinates parsed during SmartScan import, requiring no manual annotation. Clicking on a thumbnail opens the corresponding tilt series detail view.
Card view gallery
Tilt series within a grid are displayed as a thumbnail gallery with acquisition metadata (number of tilts, dose, pixel size) shown beneath each card. Clicking a tilt series opens a detail panel showing all available thumbnails, quality plots, metadata, rating controls, and processing history.
List view
An alternative tabular view provides a compact listing of tilt series with sortable columns for metadata, processing status badges (pre-processed, aligned, reconstructed), tag labels, and links to detailed views. An expandable row displays the raw tilt series thumbnail, aligned series thumbnail, alignment residual plot, and defocus plot side by side, allowing rapid evaluation of alignment residuals and CTF fit without opening external tools or navigating to separate pages.
Automatically generated thumbnails
CryoNAV generates visual previews for each data stage:
- Raw tilt series: central frame extracted from the stack
- Motion-corrected series: central slice of the aligned stack and an animated preview cycling through frames
- Aligned tilt series: animated view cycling through tilts to assess alignment quality
- Alignment residuals: residual error versus tilt-angle plots
- CTF estimates: defocus versus tilt angle plots with fit quality indicators
- Tomographic reconstructions: orthogonal XY, XZ, and YZ slices through the volume center
- Denoised tomograms: central Z-slice extracted from the denoised volume, displayed alongside the undenoised reconstruction for direct comparison
When facility-processed data is available, thumbnails are generated from those outputs immediately upon import, providing instant visual feedback without requiring the user to run any processing. Once the user's own processing completes, CryoNAV-generated thumbnails replace the facility previews.
3D visualization via 3dmod
For inspection of image stacks and tomograms (raw tilt series, aligned stacks, reconstructed volumes) and for building fiducial and boundary models, CryoNAV launches IMOD's 3dmod viewer as an external application. Rather than implementing a limited web-based volume viewer, this leverages 3dmod's full capabilities (model building, isosurface rendering, slicer tools) that cryo-ET researchers already rely on. See Integration with Cryo-EM Tools for the IMOD dependency.