Overview
About IGOR Pro
Versions:
    What's New
Features
Imaging
    Acquisition
    Analysis
    Modification
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Image Acquisition
The software interface allows all five of the user selectable data channels to be displayed simultaneously. Additionally, there is no grand difference between trace and retrace, they are both collected, and either one or both are displayed and saved based on your settings. This means that you can display and save 10 images in one scan. Currently, no other AFM software performs this function. There are three selectable user input channels with two of them for simultaneous data collection. There is also an interface to a crosspoint switch in the controller.  This crosspoint switch allows you to map out which signals are connected to which. You can easily apply specific electronic filters to the data channels that require it.  Also, the scope trace of the trace and retrace are shown along with each image. Additional features include:

• a log of all scan parameters changed during the scan which is saved in the data header.
• drift calculation and compensation being applied between scan images automatically.
• built in digital Q control with easy to adjust parameters that can be changed during scanning.  (See Digital Q Control application note)
• New! Ortho Scanning. No more need to use Grandma's raster scanning. Ortho scanning is a perfect example of how we at Asylum handle software upgrades. A customer asks for something, which requires the scans to be more precise than raster scanning would allow.  So within a few weeks we have a new installer ready that scans in orthogonal mode. You ask, we deliver. No hardware upgrades, no extra cost, just the data you need, fast.

Image Analysis
Display: Image and surface plots are available, both with standard and custom colormaps.  Surfaces can also be rendered using a different image to determine the colormap.  For example you can plot the height as the surface with the phase used for the color. This makes it easier to visually determine correlations between the data channels.  Browsing of thumbnails of the images is also supported.  You can quickly switch between different data channels displayed, as well as choose between trace, retrace or the first one available.  Roughness of the image and masked image are simultaneously available, with a wide range of statistical values provided. These include RMS, standard deviation, average, skewness and full range. 

By comparing the values obtained from the masked image and the full image, you can quickly see which regions are affecting your statistical values, allowing you to determine the roughness of your data more accurately.  Sections of straight lines as well as hand- drawn can be easily obtained.  The free hand sections allow you to trace out single molecules on the surface to determine their entire length and statistical height (see Figure 1). 

In addition, sections can easily be obtained by averaging over a user defined width.  This allows much greater statistical robustness to width and height determinations.  Both your masked images as well as the full image can also easily be converted to histograms.  Multiple distributions cans also be overlaid on the same graph for easy comparison, making trends in your data easier to spot.

Image Modifications
Standard. All of the modifications listed below can be applied to multiple images automatically.  No more opening on image, flattening it, saving it, and moving onto the next image.  Simply open them all up, which takes about three clicks, then flatten the ones you select, again about another three clicks. Additionally, an interface is provided that will allow you to define modification macros.  Often times the exact tweaking of your data is a bit of an art, but once the desired sequence is determined, you will want to apply that modification sequence to many of your images.  Our interface will allow you to do that quickly and easily. The software also allows:

- Flatten of masked / unmasked images up to 3rd order.
- Planefit of masked / unmasked images up to 3rd order.
- Erasing of scan lines.
- A wide variety of image filters, including Gaussian, median, gradient, sharpen, as well as conversion to angles.
- Also included is an easy interface to apply custom matrix convolutions.
- The masking can be done both by manually drawing regions to include or exclude, but also a variety of methods are provided to calculate the mask for you.  Additionally the masks can be quickly eroded or dilated.
- Modification history. You can undo the last modification, as well as restore your data to the original state.  Additionally, you can undo intermediate steps of your modification sequence.  This makes the image modification process faster and more robust in that you can easily see which steps are altering your data in undesirable ways.