Modify Panel. Flatten Tab

Transcription

1 AFM Image Processing Most images will need some post acquisition processing. A typical procedure is to: i) modify the image by flattening, using a planefit, and possibly also a mask, ii) analyzing the data with the roughness, section, or histogram features, iii) creating a 3D plot if necessary, iv) exporting the data in a layout or other format. These functions and others are described below. 1) To open saved data, go to MFP IP on the top pull down menu and select Browse. 2) Select the path that corresponds to the location of your saved data, and click the That s It button. 3) Select the data that you would like to analyze by double clicking on its thumbnail image. 4) This opens a Display window with tabs that include all images saved (Height, Amplitude, Phase, etc.). Some useful buttons are shown at the top of the Display: a. Range: adjusts Z scale. b. Offset: adjusts where the center of the Z range is relative to the color table; this allows more flexibility with image contrasts. c. Color Bar: the checkbox allows the Z range color table gradient to be viewed. d. The Auto button auto scales the Z range and offset. e. The ColorMap pull down menu offers many color tables to display the image data with. f. Stored data channels are listed as tabs just above the image. g. 3D: ARgyle 3D rendering. See further description below. h. Command Functions: The Commands pull down menu offers a large variety of functions such as saving images, cropping images, and exporting images. i. D: Display Panel where images can be more easily managed when there are many open in the software. j. M: Modify Panel where flattening, planefit, masking, filtering, FFT etc. is performed. See further description below. k. A: Analyze Panel is where roughness measurements, line sections and histograms of pixel data are created/ displayed /generated. See further description below. l. L: List panel allows you to open images, change directories, save images, rename extract images. m. N: Note Window where every conceivable imaging/ system parameter can be viewed. n. Ly: Export to Layout This is a feature that lets electronic notebook style pages be prepared for export. See further description below. Modify Panel 1) Many images will need to be modified to remove any background tilt, scan lines, etc. 2) Click on the M button at the top right of the Display window to open the Modify panel. 3) Most images will require flattening (to some order), a plane fit, masking, and a final flatten to properly process them. A brief description of these processes is given below. Flatten Tab 1) Start with a Flatten Order of 0 or 1 and the All Radio button selected. (A zero order flatten will subtract a number (the average value for that line of data) from each line of data. A first order flatten will subtract a line, a second order flatten will subtract a second order polynomial, etc. Choose a flatten order that seems to best describe your substrate.)

2 2) Click the Flatten button; after a brief moment of Igor calculation, the image will be flattened. 3) Depending on the data features in the flattened data, there may be flattening artifacts (streaks) around tall surface features. To remove these features a planefit and image Mask are most likely needed (described below). Planefit Tab 1) Confirm the planefitting order is set to 1 in the pulldown menu. This is the most common plane fit order for data processing. 2) Click the XY button; this will planefit the image in the X&Y plane with respect to Z. Alternatively, if the plane fit can also be performed on solely on the X (fast scan axis) or Y planes (slow scan axis). Mask Tab Image masks save a great deal of time when omitting features from images that would otherwise create flattening artifacts. Essentially, the mask picks a defined plane in the Z axis and omits anything above, or below that threshold value. The mask can also be used to do image processing exclusively within or outside the mask. 1) Confirm that Iterative is chosen in the Calc Method pull down menu. This mask type is a good mask to start with to ultimately find the proper threshold value. 2) Click the Calc Mask button; Igor will determine a Z range that is generally close to the Z range that is needed to help clean up the image. Notice the Calc Method has changed to Manual because a Z threshold value has been determined by the software. 3) Check the Fill Mask checkbox to fill the area of the image that will be masked. It s easier to tell what is masked and what is not with this box checked. 4) You may also need to check the inverse checkbox if the mask has selected the low regions in the image, and you want to mask out the tall regions. 5) At this point, you may or may not be happy with the Z range the calculation picked there are many ways to combat this: a. Manually enter a threshold range, and re calculate the mask. b. Click the Erode Mask button this will make the mask a little smaller. c. Click the Dilate Mask button this will make the mask a little larger. 6) The image can be re flattened at this point to clean up any flattening artifacts (dark horizontal streaks on the same line as a tall feature). Typically a first order flatten with the Mask button selected is performed to get rid of the dark streaks/bands. 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. 1) Expand small area around line(s) to be erased. (Click and drag a box. Right click insid it and select Expand.) 2) Go to the Erase tab of the Modify Panel. 3) Click the Draw Lines button. 4) While holding the left mouse cursor down, place the pointing finger cursor over the scan line you wish to remove, and release. Notice the line goes from red while positioning to blue when set. If

3 one line isn t enough, increase the width to two using the Line Width setvar window. If placement of line is dissatisfactory, click the Clear Lines button to remove and repeat attempt. 5) Once you are satisfied with line placement and width, click Erase Line button. 6) With the cursor over the image, click Ctrl + A to restore to original size, and assess the results. Analyze Panel The Analyze panel is where roughness, area calculations, line sections & histograms of image pixels can be viewed. To open the panel, click the A button in the Display Window Roughness Tab 1) The most recent image will have its Stats displayed in the Roughness tab. See help buttons for in depth descriptions of Stats. 2) If the image is masked, then the Masked Image column will have the Stats for the masked image as well. USEFUL NOTES ON THE ROUGHNESS STATS: a) RMS roughness: Z scale data that must be centered around 0 and must be raw data. On flattened / processed data, the RMS value then becomes the Standard Deviation data. Unfortunately, RMS roughness data has been erroneously used by the AFM community for years, probably due to a precedent set by Digital Instruments/ Veeco that has been propagated throughout the years b) Standard Deviation (SDev): removes any offsets in the Z data and looks for the points between minima and maxima. This is a better roughness parameter to use because it works with processed data, as well as data not centered around zero (what ever that dimension might be (distance, phase, current, etc.) c) Average Deviation (ADev): this is an average of the Z data points in the image data matrix. This typically is a smaller value than the SDev. d) More information is available by clicking on the question marks to the right of each data parameter. 3) Click the Export Roughness button to create a text file of the Stats, and dump it wherever the stored image is saved. Section Tab The Section tab is where to perform line sections lines can be of user defined lengths, full vectors across the image, free hand, or averages of scan lines. The lower portion of the panel will show the Stats on the Igor cursors ( X, X ), relative to each other in three dimensions. 1) Open the Analyze Panel by clicking the A button in the Display window. 2) Open the Section tab. 3) The Mode pull down menu offers vector type lines or free hand lines to be drawn. 4) Select Line from the Mode pull down menu. 5) Click the Draw button. 6) Pull cursor over image to draw a line on the feature of interest in the image.

4 7) Select Full Width checkbox if it is desired for the line section to extend to the edge of the scan area. 8) Multiple scan lines can be averaged to eliminate noise or give more statistical relevance to the sectioned line by changing the width of the line (number of pixels) just to the right of the full width check box. 9) Once the line is drawn, a Section plot will appear. The Igor cursors (Ctrl + I ( X, X )), can be placed on the curve to measure points on the line (notice blue cursors on the features in image correspond to cursors on the line section). Their respective cursor location Stats are displayed in the lower half of the Analyze panel, and dx and dy values are given at the bottom of the section plot. 10) Click the Export Table button to get these cursor stats. These can be saved as a text file, or dumped into various types of software for further organization. 11) If the image happens to possess some tilt, it won t be intuitive to get a proper height from the cursors. There are two ways to get around this: a. Perform a 1st order XY plane fit on the image. Most of the time this will fix the problem. If it doesn t, proceed to the next step. b. Hold Ctrl key over curve to be leveled ; a cursor will appear; right or left mouse click over line, and move to make image flat. From here, the Igor Ctrl + I cursors can be put on to measure a more accurate height differentials. 12) To export line sections as XY data: a. Click the Edit button in the Section plot this will bring up a table with a Y value, relative to the points in the Igor Wave, and the points where the blue cursors are (kind of meaningless for use with another spreadsheet). b. Go to Windows > New Table c. Select SectionWaveX & SectionWaveY; d. Click Do It this will create an X,Y delimited table from which can be cut and pasted into any spreadsheet program. Histogram Tab The histogram tab allows image pixels to be counted and presented. This is analogous to Bearing analysis found in other commercial AFM software. 1) With an image open, select New from the Make Histogram pulldown menu. 2) The Histogram Graph will appear with pixel count (Y) relative to Z scale (X). This panel has a fair amount of features. You can change the bin size, try fitting the data with peaks, etc. 3D Images ARgyle is the MFP 3D s 3D image rendering software that uses open GL source code. It can produce some remarkable AFM data representations in real time or with offline analysis with custom colors & specular lighting. It also allows multiple data channel overlay as a fourth color dimension to correlate with surface topography. 1) Click the 3D button at the top of the display window tab that has the (processed) data that you wish to display in ARgyle. This will bring up the Master ArGL Panel and the ARgyle 3D rendered image. 2) Click on the 3D rendered image, left mouse click and rotate it to an orientation you are happy with. 3) In the Display tab, choose an appealing color from the ColorMap pull down menu; Notice you can invert the Z scale or color. Custom colors tables can also be generated by choosing Define Custom.

5 4) In the View tab, select None from the Clip pull down menu; choose Zoom from the View Mode pull down menu. Check the Aspect 1 checkbox. This will scale the Z data to the XY data. If this isn t enough Z scaling, adjust the Z scale parameter to larger value. A Z scale of 0 will effectively create a 2D image. 5) In the View tab, select Data Scale from the View Mode pull down menu. Here you can adjust the Z scale of the data just as you can in the display window use left vertical slider bar, or data scale setvar. The Data Offset essentially where the plane of the image sits within the color scale (color bar). 6) To add Specular lighting, go to the Lights tab, click the shiny check box. The percent of specular light can also be defined in the Factor setvar. Lighting (either normal or specular) can be adjusted by holding the right mouse over the 3D rendered image, and moving it around the image until an appealing angle is achieved. Adjust light to hide scan lines for better presentation. 7) The light rotation and pitch setvar values can be viewed in the Light Rotation sub tab of the View tab. 8) Axis fonts, font sizes and background colors can be adjusted in the Prefs tab. 9) Activating the All checkbox in the upper left corner of most tabs, applies the ARgyle parameter settings to all open images. 10) The image can be set to spin automatically. a. Select Spin from the View Mode pull down menu in the View tab. b. ARgyle image axes, and ticks can be adjusted in the Axes tab. 11) To overlay multiple channels: a. In the New tab of the Master ArGL Panel, choose the image and image channel you want the topography to be displayed (i.e. the image that will have 3D rendering to it). b. Process your two channels to your liking (i.e flatten, mask, pick colors). Create an ARgyle image for each image channel. One of the channels needs to be grayscale (height), while the other is some color (phase). Adjust the z scale to 0 for the color channel c. Click the color checkbox, and then choose the same image file, and the other data channel that you want to over lay. Make sure to keep the same direction in the overlay for proper registration (i.e. Trace with Trace). 12) The are many ways to export images from the ARgyle window: a. Make the 3D image window the forward most image (active window), Copy to clipboard, and dump into another program (Paint, Photoshop, PowerPoint, etc.) ORb. Go to the Edit menu of the Main Igor tool bar; select Export Graphics select type of file you want to export it as (TIFFs are larger files than JPEGs, but they are lossless) ORc. Click Export to Layout button in New tab of the Master ArGL Panel. 13) Additionally, the MFP 3D software has these items called Layouts. Any data you have worked up in the offline analysis can be dumped into one of these layouts by click the layout button. a. Most windows have a Ly or an export to layout button that you can use to dump the data into a layout. (2D or 3D Images, section plots, histograms, etc.) b. To save the layout, go to File > Save Graphics. The Save Graphics File dialogue comes up, where you can determine what file type to save the file as; the name; and the Path. c. The layout can then be called up promptly as an image similar to a page in a notebook.