Scanning Probe Microscopy Facility

Origin AFM Analyze Image

Analyze Panel

Analyze Panel toolbar with functions described in the text.
Analyze Panel toolbar with functions described below.

Roughness

The roughness for the full image is already calculated and displayed, but a mask can be made to exclude certain areas from the roughness in the image.

  1. Click on the Mask Make button. This will make a box on the image.
  2. Adjust the box size and X:Y ratio of the box as needed.
  3. Use the blue slider bars to move the box around the image.
  4. Click Calculate Roughness. All of the calculated data will appear in the Masked Image Column.
  5. Click Export Roughness to save this data as a text file. The program will not prompt to rename the file, it will use the title of the image and append "Roughness" to the end.

To Use a Custom Shape Mask

  1. Go to the Mask Tab in the Modify Panel.
  2. Clear any existing mask by clicking Reset Mask.
  3. Select the type of mask to be made.
    1. Calc Mask - Adjust the threshold as needed.
    2. Exclude Points
      1. Use the various shape drawing tools that appear to the left of the image to draw around the area(s).
      2. Click Make Mask.
  4. The area in red is now excluded from the roughness measurements.
  5. To invert the selection, check (or uncheck) the Inverse box in the Mask Tab.

Section Analysis

  1. Set the Mode to Line.
  2. Unselect the Angle checkbox.
  3. Click Draw.
  4. Click on the image. Click “Make Graph” if a graph does not automatically appear.
  5. Drag the red cross hair (⊕) and green box (☒) markers to adjust the location of the section analysis line.
  6. To shorten the section analysis, uncheck the Full box in the Section Tab.
  7. To save the graph data:
    1. Click Edit in the Graph Window.
    2. Click anywhere in the raw data window.
    3. Select File > Save Table Copy.
    4. Navigate to the desired folder.
    5. Enter a filename.
    6. Change the file type to .csv or .txt.
    7. Click Save.
  8. Click Clear to remove the line from the image. Drag the red and green markers to the edge of the image to remove them.

Note: Image tilt can become very apparent from line sections. Doing a planefit can correct this, or a subtraction of a linear background can be done manually to the section data.

To manually correct the tilt, hold "Ctrl" while moving the mouse over the curve until an up/down arrow cursor appears. Click and drag to manually level. This modification will be undone if the section is changed.

Other Functions

Rotating Images

  1. Click on the Commands Menu of the image to be rotated.
  2. Select Extract Layer. The layered image will show up in the List Panel as a new image named “LayerData.” A command window will pop up after the layer has been extracted.
  3. Double-click on LayerData in the List Panel to open the image.
  4. In the Command Window, type RotateImage(LayerData,Degrees)and press Enter.
    1. Degrees is the angle to rotate the image (10, 35, 180, and so on).
    2. To undo a rotation, type the same command but add a minus sign before the degree number.
  5. Save the Rotated Image separately as a TIF/PNG/JPEG.

Cropping Images

Cropping will delete excess data, so it is important to save the original raw data by doing the crop on an Extracted Layer.

  1. Click on the Commands Menu of the image to be cropped.
  2. Select Extract Layer. The layered image will show up in the List Panel as a new image named “LayerData.” A command window will pop up after the layer has been extracted.
  3. Double-click on LayerData in the List Panel to open the image.
  4. In the Image, Click and drag a box over the area of interest.
  5. Right click in the box and select Expand.
  6. Click on the Commands Menu .
  7. Select Crop Image.
  8. Save the Cropped Image separately as a TIF/PNG/JPEG.

ARgyle Light 3D Rendering

From the main Asylum Research Program, the 3D renderings can only be saved by exporting them to the layout. It is more convenient to open the 3D renderings in the ARgyle Light Program (located on the desktop). From there the renderings can be saved much more easily as a JPEG, PNG, TIFF, ASCII, STL, or VRML files.

  1. Open the ARgyle Light Program.
  2. Click File > Open .
  3. Navigate to the .ibw File of the image .
  4. Select the Data Stream to be rendered from the drop-down menu at the top left.
  5. Adjust the properties of the rendering with the options at the bottom of the window. Color can be adjusted in the drop-down menu next to the data menu.
  6. Click Image > Select the file type to save the rendering as Export… > saves as a basic image type (JPEG, PNG, TIFF, BMP).

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