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This user guide contains the information on how to install, configure and run the Ranger peak-finding code. Ranger is continually being improved based on user feedback so please check the support page for update notifications and changelogs.

User Manual Quick Links:

Installation    -    Configuration    -    Running Ranger    -    Results


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Ranger Component Files

Ranger is continually being improved based on user feedback. To facilitate this it is built from several modules each of which can be updated separately. The table below outlines the files that you should have in your installation, their purpose and the most current version. Before running Ranger the user should check all these files are present in the same folder along with the image file to be processed.

File Purpose Current Version Release Date
Ranger_Wrapper Sets up the user variables for the image restoration. 2.2 12th September 2013
Ranger_Core Performs the image restoration. 2.2 12th September 2013
Ranger_license_check Checks the current license state. 1.0 12th September 2013
File_Opener Opens image files of various types and passes image data to "Ranger_Core". 1.5.3 21st June 2013
ReadDM3* Allows "File_Opener" to handle Gatan .dm3 files. - 19th March 2010
serReader* Allows "File_Opener" to handle Titan .ser files. - 6th August 2009


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Ranger Wrapper - Setting up Search Variables

The Ranger wrapper file sets up all the input variables needed to search the image to the user’s specification. Before running the code each of the variables should be verified. The following table defined the action of each input variable.

Variable Purpose Default / Recommended Value Input Restrictions Notes
refinePositions Allows the user to select whether to refine the estiamted positions by 2D Gaussian fitting 0 0 for off, 1 for on -
show_progress Allows the user to decide whether to show progress figures during the processing 1 -
display_results Allows the user to choose to display a large results window after processing has finished 1 -

Running Ranger

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Once the desired parameters have been selected in the Wrapper file, simply press 'Run' (or F5). The code will then begin searching for the optimum feature-feature separation. If the user has selected to show the progress of the search a window will be displayed that will update with each new trial feature-separation. The left panel will show the raw data with the evaluated feature positions overlaid. The right panel will show a plot of the number of features identified for each trial spacing. At any given time the current estimate of the optimum spacing is indicated by the small blue circle in the right panel. If the user presses the cancel button to terminate the search early it is this value that will be used.

It is normal for too many features to be found initially as the code determines the true feature spacing.

Once the optimum value is found the peak-finding runs once more. An image with the determined points overlaid will be displayed. Next, the user has the option to click on any missing peaks using the mouse cursor. Accidental cursor clicks can be undone using the 'backspace' button. Once happy press 'Enter' to accept the peaks. The same is repeated for the removal of any surplus peaks. Finally a confirmation message is displayed stating the number of features found.

If the user selected to perform the optional 2D Gaussian peak-position refinement the course estimates will be used as the starting coordinates for the sub-pixel coordinate fitting.

Ranger Results

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After processing the results are displayed and also available in the workspace as an 'nx2' variable containing the X and Y coordinates of the 'n' features identified.

* MatLab™ function files available from the MatLab Central file exchange.

  • The file "ReadDM3" was developed by Fred Sigworth and Liguo Wang at Yale University.
  • The file "serReader" was developed by Peter Ercius at the National Center for Electron Microscopy (NCEM).

Content © 2012 Lewys Jones - layout & design by Vincent Chan