Feature Detection step

This step allows you to optimize the detection of features by calibrating the system against a standard and setting thresholds.

21.10.1

Calibration tab - setting up the backscattered detector

The points below describe how the backscattered electron detector signal is used to set the upper and lower gray level thresholds. All features which give a signal within these thresholds are set to white and all others are set to black.

It is important to correctly set the upper and lower threshold or time may be wasted detecting unwanted features. For given detector contrast and brightness settings, lower than optimum threshold settings may increase the number of background features detected and unnecessary time will be spent on each field. Higher than optimum threshold settings may increase the chances of missing features.

Select the area defined for the calibration and beam compensation check from the drop down list. To move the microscope stage to this area, press 'Move to Area'. The type of sample you use as a reference is important. Ideally it should have the same dynamic range over a given area as that over a typical area of your sample on which you wish to detect features.

Turn off the auto brightness and contrast on your backscattered detector. Press the start button to start continuous image acquisition. A live backscattered image of the area will be displayed and acquisition will continue until the stop button is pressed.

A line is automatically drawn on the image. Click and drag to move the ends of the line across a feature or features of interest. The adjacent graph shows the distribution of signal intensity across the linescan. Adjust the backscattered detector gain and offset in order to optimize the signal level. Adjusting the gain (contrast) will increase or decrease the separation of the plateau of the waveform. Adjusting the offset (brightness) will move the waveform up and down.

You should then set the calibration levels on the graph to appropriate values.

21.10.2 Thresholds tab

This tab allows you to setup up to six pairs of thresholds on an image. It also allows you to switch between gray and threshold images to check the feature detection.

Method

Select the position you wish to move to from the drop down list and press 'Move to Reference'. Switch off the auto brightness and contrast on your backscattered detector.

Press the start button to collect an electron image. If you have set any gray image processes, these will be applied to the electron image.

Select the number of thresholds you wish to set from this drop down list.

The histogram shows the frequency distribution of the gray level (where gray level represents the signal intensity). To set levels for the currently selected threshold, you can enter minimum and maximum gray level values directly or slide the markers beneath the image or move them directly on the histogram. Press 'Feature Detect' to apply the thresholds and image processes defined in detection setup to the current image. The features detected are colored on the electron image and the total number in each threshold band displayed.

You can display either the gray image, threshold image or feature image by selecting the appropriate button above the image viewer. You may need to check the feature detection by zooming in (from right mouse click) and swapping between gray and threshold images to see that feature edges are correct. Several zoom steps may be needed for very small features. Thresholds can also be set from a calibration standard which may be useful if the features you are looking for are rare and not found in the setup field. Note - right mouse click to show the various options available such as export facilities, full screen image display and image details.

21.10.3 Beam compensation checks

Beam current drift will affect image threshold. INCA Feature allows you to automatically compensate for beam current drift during a run by periodically returning to a calibration standard. The thresholds are then reset to compensate for drift such that features are reproducibly detected.

Method

Select the area defined for the calibration and beam compensation check from the drop down list. Select the time interval between beam compensation checks from the drop down list. This will depend on the length of the run, the predicted beam current drift and the effect on the thresholding of the image. During a run, the stage will move to this reference position, set the magnification and acquire an image. The beam rasters over a small area on the standard (green square) and the mean threshold is

determined. This value is monitored and if it changes, the thresholds are adjusted accordingly such that beam drift is compensated for. You can change the maximum deviation above and minimum deviation below starting value on the Calibration form from the Feature options accessed via 'Options' on the main

Number channels

You can select where on the Feature you wish to collect ED data from i.e., Whole feature or Center of longest chord. You should consider the interaction volume and homogeneity of the feature composition with respect to the size of the feature.

If you decide to make morphological measurements only by checking the tick box, all the ED parameters will be grayed out.

You can select the number of ED passes you wish to perform. Two pass acquisition is only relevant if you have an ED filter.

A simplified summary is given below: Feature locate

Measure feature Passes Morph filter?

Pass 1 ED spectrum acquisition Passes ED filter?

Pass 2 ED spectrum Measure feature Classify feature

If you have an ED filter set for any of your classes, you should use two ED passes. Note that the final classification is based on the two ED spectra added together.

If you have no ED filter set for any of your classes, one pass is sufficient. However if you do set two ED passes, the 'Passes ED filter' step in the above sequence is ignored and pass 1 and pass 2 are carried out. Note that the final classification is based on the two ED spectra added together.

If an ED filter is set

Setting an ED filter allows features to be rejected based upon Pass 1 ED analysis. Features deemed 'interesting' after the first pass can be analyzed for much longer (Pass 2). In this situation, you should set the number of ED passes to 2.

If 'Use in ED filter' is marked Yes for a class, the class will be evaluated after a short ED acquisition step (Pass 1). If a feature is found to be a member of this class, then further ED analysis of the feature may be performed (Pass 2)

Note that a feature, its associated morphological results and its preliminary quant results based on Pass 1 spectrum are stored in the database even if it is rejected by the ED filter. In this case, features are stored in the 'Rejected ED' class.