Quick Start with an Example

For simplicity, a synthetic dataset will be used in the following demonstration. It illustrates only the basic functionality of the program. More advanced features will be introduced in detail in the sections that follow.

  1. Launch the program by the command "signature".
  2. Define a new project space (Menu: Project: New), and name it "TEST". A directory "TEST.ems" will be created at the specified location, together with a set of sub-directories. All directories and files in the project space are managed internally by Signature. The "Project" label at the upper right corner of the GUI window now becomes "TEST".
  3. Load micrograph "synthetic.mrc" (from Menu: Data: Micrograph: Load MRC). The "Film" label at the upper right corner of the GUI window becomes "synthetic".
  4. Load template image stack "templates.mrc" (from Menu: Data : Template: Load MRC). In Circular Masking box, set LCF profile radius to 0.7, and SCF profile radius to 0.6, then click Apply.
  5. In Rotational Search box, set Interval to 5 degrees.
  6. Click the Particle button at the bottom of the GUI window, switching to the screening page.
  7. In Particle Parameters box, change Resize to 2. Click the Screening button. The system becomes busy, as indicated by the red light at the bottom right corner of the GUI window. Once the task is completed, the indicator becomes green.
  8. The number of identified particles is displayed at Particle Count under the monitor. Change the LCF and SCF threshold slidebars at will and observe the effect.
  9. To inspect the particle selection through the monitors, click the Accept (CTRL+a) and/or Reject (CTRL+r) buttons. Undo (CTRL+u) will take one step back. The Score bar displays the best matching score of the current selection with the template images. The automatically selected particles are marked by red crosses, and the accepted selections are marked by green crosses.
  10. Set the display scale and blurring to various levels to achieve the best visual perception. Remember to press ENTER to trigger the update.
  11. Toggle the cross-hair display in the monitors by the + button under the monitor. The distance between the two pairs of short-bars indicates the particle's diameter as specified at Size in Particle Parameters box. The distance display is also affected by the pixel size of the image, which is defined in Micrograph OpPanel.
  12. Turn on the S button under the monitor, and the image spectrum will be displayed. If a particle selection is too close to the edge of the micrograph, the spectrum will not be shown.
  13. Turn on the T button under the monitor, the best matching template will be displayed.
  14. Save the particle selection into an MRC stack (Menu: Particle: Save Image Frames). The file is named "TEST.ems/particle/synthetic.mrc".
  15. Open the particle selection in Image Stack Editor (Menu: Function: Image Stack Editor), click the New button in the panel to load the file.
  16. To normalize the image intensity to N(0, 1), click the Norm button in Image Processing box.
  17. To save the processed image stack to a new file, click the Save button and type in a file name.
  18. Close this project (Menu: Project: Close), and answer "Yes" when prompted to save the project.