SerialEM Help Topics

General Topics

Introduction to SerialEM
Mouse and Keyboard Controls
Control Panels
Image Acquisition from CCD Cameras and Direct Electron Detectors
Acquiring Tilt Series
Using and Troubleshooting Autofocus
Low Dose Mode
Energy Filtering
Using the Navigator
Acquiring Multiple Tilt Series Automatically
Settings Files
Script Commands
Scripting with Python
Hiding and Disabling Menu and Dialog Items
Setting Up SerialEM
Property File Entries
Metadata and Navigator File Formats and Other Documentation

Menu Commands

File menu
Settings menu
Camera menu
Calibration menu
Focus/Tune menu
Script menu
Tasks menu
Tilt Series menu
Process menu
Navigator menu
Tools menu
Window menu
Help menu

Control Panels

Buffer Status panel
Buffer Control panel
Image Display Control panel
Microscope Status panel
Microscope Control panel
Tilt Control panel
Camera & Script Control panel
Image Alignment & Focus panel
Low Dose Control panel
Montage Control panel
Filter Control panel
Direct Electron Camera panel
STEM Control panel

Dialog Boxes

Acquisition-related dialogs
   Camera Setup dialog
   Frame File Options dialog
   Frame Summing Selector dialog
   Frame Alignment Parameters dialog
   Gain Reference dialog
   Direct Electron Server Reference Maker dialog
   Gain Reference Policy dialog
   Montage Setup dialog
Tilt-series-related dialogs
   Tilt Series Setup dialog
   Dose Symmetric Tilt Series Parameters dialog
   Tilt Series Scheduled Changes dialog
   Tilt Series Resume dialog
   Tilt Series Back Up dialog
   Tilt Series Extra Output dialog
   Tilt Series Batch Policies dialog
   Tilt Series Range Finder dialog
   Tilt Series Range Viewing dialog
Navigator-related dialogs
   Navigator window
   Navigator Acquire dialog
   Navigator Import dialog
   Shift to Marker dialog
   Align with Rotation dialog
   Navigator Align Setup dialog
   Imaging State dialog
   Multiple Record Setup dialog
   Step and Adjust IS Setup dialog
   Hole Finder dialog
   Multiple Hole Combiner dialog
   Autocontouring Grid Squares dialog
Other dialogs
   File Properties dialog
   Read Current File dialog
   Script Control dialog
   Script Editing window
   CTF Fitting Parameters dialog
   Beam Autocentering Setup dialog
   Specimen Cooking Setup dialog
   Wait for Drift Setup dialog
   Eucentricity by Focus dialog
   Phase Plate Conditioning Setup dialog
   Dewar and Vacuum Management dialog
   Coma vs. Image Shift Calibration dialog
   Stage Move Tool window