Display & Process a Micrograph

Access: CP::Micrograph::Micrograph (Tab) and CP::Editor::IMG




There are two ways to load and display a micrograph, depending on its status in the project space:

The intensity and contrast of the image display can be adjusted via the dials located at the lower-right corner of DP.


Quality Inspection

The quality of an image can be assessed by its intensity histogram and power spectrum.  Note that the metrics are simple to use, but not sufficient for a comprehensive quality assessment.  The Histogram button will activate the image intensity histogram display and the Spectrum button will evaluate the power-spectrum for a selected region (CTRL+LeftClick to define the box center), with the square dimension being set at Box-Size (in pixels).


Image Masking (Tab)

In computational particle screening, the masked area (beneath a semi-transparent yellow layer) in the micrograph will not be searched for particles.  The mask display can be toggled by the M (masking) button in the Image Toolbox at DP::ToolBar.  The micrograph mask can be created either manually or computationally:


Image Cropping (Tab)

A region of interest (ROI) in a displayed micrograph can be cut out and saved into a new image file (MRC).  To crop the image, switch to the cropping tab and select either the "rectangle" or the "filamental" shape.  Then, mark a ROI by the keyboard/mouse combination CTRL+LeftClick+Drag.  The selected ROI will be display in CP::Monitor, which can then be saved by the Save button at the bottom of the tab.  The Clear button resets the monitor display.


Taking Notes

Key information about a data micrograph (e.g., imaging setup and image quality) can be recorded in the Notes text-box for future reference.  The notes will be retrieved automatically whenever the micrograph is highlighted in the DataView spreadsheet.


Image Processing Functions

Numerous functions for 2D image processing can be accessed from the pull-down menu.  After selecting a function and setting its associated parameters, press the Apply button to active the image processing function.  Upon completion, the image display in DP::MainDisplay will be updated to reflect the result.

These image-processing functions will introduce changes to the image pixels and update the display afterwards.  However, the resulting image is not automatically saved back to the original file.  It is at the user's discretion to export the result to an image file.  As a safe-guard, PARTICLE will prompt to save a modified image upon closing.


Demonstration

To display and filter a micrograph in the project space of the demo dataset,

  1. Start the PARTICLE program;
  2. Open the project space from CP::MenuBar::Project::Open, go to the folder "test.em/" and select the project definition "project.sys";
  3. All micrograph data will be loaded into the DataView spreadsheet;
  4. Select the image T1001 by mouse LeftClick to highlight the entry;
  5. Activate the Display button (below the spreadsheet), the image will be displayed in DP and the CP control will be switched to Micrograph::Micrograph;
  6. In the Masking tab (at the lower-right region of the page), set Border Margin to "4", then press Clear;
  7. In the Image Processing group (at the lower-left region of the page), select Gaussian Filter, set Sigma to "0.7", then activate the Apply button.

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