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.
- Launch the program by the command "signature".
- 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".
- Load micrograph "synthetic.mrc"
(from Menu :
Data :
Micrograph : Load MRC). The
"Film" label at the upper right corner of the GUI window becomes
"synthetic".
- 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.
- In Rotational Search
box, set Interval
to 5 degrees.
- Click the Particle
button at the bottom of the GUI window, switching to the screening page.
- 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.
- 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.
- 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.
- Set the display scale and blurring to various levels to
achieve the best visual perception.
Remember to press ENTER to trigger the update.
- 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.
- 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.
- Turn on the T
button under the monitor, the best matching template will be displayed.
- Save the particle selection into an MRC stack (Menu
: Particle : Save Image Frames). The file is named
"TEST.ems/particle/synthetic.mrc".
- Open the particle selection in Image Stack Editor (Menu
: Function : Image Stack Editor), click the New
button in the panel to load the file.
- To normalize the image intensity to N(0, 1), click the Norm
button in Image
Processing box.
- To save the processed image stack to a new file, click the Save
button and type in a file name.
- Close this project (Menu
: Project : Close), and answer "Yes" when prompted to save the
project.
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