Appendix 1—table 1. Input parameters for a SmartScope session.
Parameter names and their description. This is presented as a form on the web interface. These parameters can also be updated during the imaging process.
| Parameter name | Description |
|---|---|
| General session parameters | |
| Session name | Name of the microscopy session |
| Group | Group name of the microscopy session. Usually the principal investigator’s name |
| Microscope | Microscope being used for the session |
| Detector | Detector being used for the session |
| Collection parameters | |
| Atlas X | Number of tiles for the Atlas acquisition in X axis (default: 3) |
| Atlas Y | Number of tiles for the Atlas acquisition in Y axis (default: 3) |
| Square X | Number of tiles for the window acquisition in X axis (default: 1) |
| Square Y | Number of tiles for the window acquisition in the Y axis (default: 1) |
| Squares num | Number of windows to be selected for high-magnification imaging (default: 3) |
| Holes per square | Number of targets per windows to be selected for higher-magnification imaging. If 0 is entered, all targets will be selected and data collection mode will be enabled (default: 3) |
| BIS max distance | Beam-Image shift grouping radius in microns (default: 0) |
| Min BIS group size | Smallest Beam-Image shift group size to be considered (default: 1) |
| Target defocus min | Lower end of the defocus range for rolling defocus in microns (default: –2) |
| Target defocus max | Higher end of the defocus range for rolling defocus in microns (default: –2) |
| Defocus step | Step by which the defocus is varied between each target group (default: 0) |
| Drift crit | Drift threshold to be met during the drift settling procedure before proceeding with high-magnification imaging. Use –1 to disable (default: –1) |
| Tilt angle | Tilt angle to use for high-magnification imaging. Works with BIS enabled (default: 0) |
| Save frames | Whether to save the movie frames or return aligned sum (default: Saving enabled) |
| Zeroloss delay | Time delay in hours for zero loss peak refinement. Only useful if the microscope has an energy filter. Use –1 to deactivate (default: –1) |
| Offset targeting | Enable random targeting off-center to sample the ice gradient and carbon mesh particles. Automatically disabled in data collection mode (default: enabled) |
| Offset distance | Override the random offset by an absolute value in microns. Can be used in data collection mode. Use –1 to disable (default: disabled) |
| Autoloader (1 per grid) | |
| Name | Name of the grid |
| Position | Position in the autoloader |
| Hole type | Grid hole spacing type (i.e. R1.2/1.3) |
| Mesh size | Grid mesh size and spacing (i.e. 300) |
| Mesh material | Grid mesh material (i.e. carbon or gold) |