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Pore Size Distribution on a Scanning Electron Microscope Image

In this lesson Able Image Analyser will be used for automated measurement of pore sizes in the SEM image "SEMPores.jpg" (If you are using an old version of the program the image the image is NOT included in the Sample images folder. Download it from here: SEMPores.jpg)
  1. Open file SEMPores.jpg.
  2. Perform spatial calibration: Spatial calibration will calculate the conversion factor from pixels into nanometers. It is described in the example Manual linear dimension measurement. Correctly performed spatial calibration will reveal that 1 pixel of the image represent 0.129 nm in the image.
  3. Calibrating SEM image

  4. Cutting the image: We have to get rid of the SEM information bar in the lower part of the picture. Use selection tool to select the rectangle that includes just the SEM image. Then use menu Edit - Copy and Edit - Paste as a new image to obtain new image.

    Selecting the rectangular part of the image

  5. Filtering: Because the SEM image is noisy it has to be filtered a bit before further analysis. Use menu Filters - Normal Filters - Soften (5x5) to reduce the graininess.

    SEM image filtering

  6. Binarisation: The image has to be binarized using thresholding procedure. Click menu Binary-Threshold to show the intensity histogram. Click (and drag) the left mouse button on the histogram to change the threshold level. When the proper threshold is selected just the pores should be colored red. A good threshold level for this particular image seems to be around 70.

    Selecting proper threshold for image binarisation.

  7. Choosing parameters of analysis: Once you have the binary image click menu Binary - Analyse Objects. Set the minimum particle size to 200 pixels (to avoid analysis ofsmall noisy chunks in the image) and maximum particle size to 1000000 pixels (to include big objects). Click OK.

    Choosing analysis parameters

  8. Analysis results: The program will display outlines of all detected objects in the image and the spreadsheet windows with analysis results for each objects.
      The columns include:
    1. A: Object index
    2. B: X-Coordinate of the object center (in nm)
    3. C: Y-Coordinate of the object center (in nm)
    4. D: Size of the object (in square nm)

    Results of the image analysis with Able Image Analyser

  9. Data export: The results of the analysis can be exported to text file for subsequent analysis in other programs, such as Excel, Origin, IgorPro, Mathematica, Matlab... To export data click menu File -> Save As in the spreadsheet window of AIA. Type in the file name and click OK.
  10. Data importis one-click away. In Excel just use File -> Open to open the file. The spreadsheet is prepared for further analysis. Results of the image analysis exported into Excel


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