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Ryan’s MFP-3D Procedural Operation ‘Manualette’ Version 10 (v080501; Igor 6.04A); 12.12 12.2.4: Erase Tab: Erasing aberrant scan lines is easily done with the MFP-3D software. Note that erasing too many lines for a publication can work against you- Experienced SPMers expect an aberrant noise line here and there in publication images. Please use this feature with discretion. Expand small area around line(s) to be erased. Go to the Erase tab of the Modify Panel. Click the ‘Draw Lines’ button. Figure 12.2.4.1: The Erase (scan lines) tab of the Modify Panel. While holding the left mouse cursor down, place the pointing finger cursor (Figure 12.2.4.1C) over the scan line you wish to remove, and release. Notice the line goes from red while positioning, and blue when set. In this example, one didn’t seem enough, so it was increased to two using the ‘Line Width’ setvar window. If placement of line is dissatisfactory, click the ‘Clear Lines’ button to remove and repeat attempt. Click ‘Erase Line’ button. With the cursor over the image, click Ctrl + A to restore to original size to assess results. • Figure 12.2.4.2 shows a very noticeable aberrant scan line in the ARgyle 3D rendering (Figure 12.2.4.2A). To erase scan lines precisely, the author finds it easier to expand on a small area(s) containing the aberrant scan line (Figure 12.2.4.2B), giving more control over placement or cursor before erasing it (Figure 12.2.4.2C). A B C Figure 12.2.4.2: ARgyle 3D rendering showing highlighting aberrant scan line; B) Expand on area where scan line is to be erased; C) Place ‘Draw line’ cursor on scan line and erase. • To increase the number of scan lines to erase, increase the ‘Line Width’ setvar value.
Ryan’s MFP-3D Procedural Operation ‘Manualette’ Version 10 (v080501; Igor 6.04A); 12.13 12.2.5 Filter Tab This tab performs various images filtering. The author doesn’t claim to have a great knowledge of image processing and filtering algorithms, but just experimenting with some of the parameters yielded the examples described below. The two filters that are mainly used are the NxN and 3x3 matirx filter widths. At each pixel of the image, they look at the nearest neighbors of that pixel, and apply an operation on those neighboring pixels to calculate the new pixel. A description of these matrix filters can be defined better in the software help menus. NxN filter pull-down: this matrix filter has various filter method types including: Median, Average, Gauss, min, max, NaNZapmedian (whatever that is…). The Size setvar defines the size of the NxN matrix; the larger the number, the longer the calculation time. The author looks at it similar to a smoothing function. Figure 12.2.5.1: Filter tab offers various matrix filter with respective image filter types and user defined processing intereations. The Passes setvar defines the number of iterations that filtering process undergoes. The 3x3 Filter pull-down (seems to) performs a 3x3 matrix filter on the image; filter types here include: Surface edges, Find edges, point, sharpen, sharpen more, and the gradient filters in each direction (N,S,E,W). • Figure 12.2.5.2 shows some examples of what the filter type methods do- the author choose to use a 10x10 matirx filter so the changes are (more or less) obvious relative to the raw unfiltered data. Respective line sections below images also show differences between filter processing. The author recommends experimenting with these parameters if image processing is needed on your data, but cannot offer much practical advice due to lack of experience filtering images.
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