Optimization

This interface allows you to setup and start recipe step (process) optimization (i.e., auto-setting determination). After selecting optimization parameters, you will be asked to enter a range for some of the process’ parameters. This will start a loop which will execute the process at each parameter combination within the specified range. The parameter combination which yields the best quality metric will be set as the new parameter combination for the process. This calculation will be re-performed for any image the Recipe is run on.

The optimization interface is available by clicking the the “Optimize” button in the top right corner of the Recipe panel. The following steps are optimizable:

Pre-Processing

• Rotate Image
• Adjust Contrast
• Smart Cluster
• Interpolation
  

Segmentation

• Basic Threshold
• Range Threshold
• Adaptive Threshold
• E-M Threshold
• Watershed
• Local Threshold
• Region Grow
• Fast Marching Method
• Find Edges
  

Morphology

• Dilate Uniform
• Dilate Smart
• Dilate Retain
• Erode Uniform
• Erode Smart
• Erode Retain
• Separate Features
• Smooth Features
  

Clean-Up

• Reject Features
  

1. Comparison Image

Image to compare processed image to during optimization

2. Smart Reference

Choose whether to apply high-pass FFT filtering to comparison image. When “On” Smart Reference with make feature edges more important, and often improves the results of your optimization.

3. View Images

Choose whether to display optimization at each step

4. Save Images

Choose whether to save each frame of the optimization movie

5. Save Histograms

Choose whether to view/save the histograms of the processed image at each step

6. Area of Interest

Choose whether to use a sub-region or the entire image for optimization

7. Metric

Choose metric to use for comparing processed image to the comparison image

• Selection Match: A fast measure of image similarity that describes how well the processed image describes the comparison image. Only available when optimizing steps which result in a selection image. Does not take into account the uncertainty of the comparison image. Better suited for simpler segmentation problems with clear contrast between features and background. The optimization will choose the parameter combination which yields a maximum Selection Match.

• Mutual Information: A more advanced measure of image similarity that describes how well the processed image describes the comparison image [1,2]. Available when optimizing steps which result in either a selection or grayscale image. Takes into account the uncertainty of the comparison image. The optimization will choose the parameter combination which yields a maximum mutual information.

• Intensity Match: A measure of image similarity between two grayscale images. Only available when optimizing steps which result in a grayscale image. Computed as the normalized correlation coefficient between both images.

8. Compare

Choose whether to use the images, or their two-point correlation functions for comparison

9. Parameter Value (min)

Minimum value of the parameter range to explore

10. Parameter Value (max)

Maximum value of the parameter range to explore

11. Parameter Value (inc)

Increment (step size) to take between the minimum and maximum parameter values

*Some functions allow for 2 or 3 parameters to be optimized simultaneously. In this case, additional sets of [min, max, inc] entries will be shown. Set the min and max equal to each other to fix any parameter during optimization.

References

[1] Rahunathan, Smriti, D. Stredney, P. Schmalbrock, and B.D. Clymer. Image Registration Using Rigid Registration and Maximization of Mutual Information. Poster presented at: MMVR13. The 13th Annual Medicine Meets Virtual Reality Conference; 2005 January 26–29; Long Beach, CA.

[2] D. Mattes, D.R. Haynor, H. Vesselle, T. Lewellen, and W. Eubank. “Non-rigid multimodality image registration.” (Proceedings paper).Medical Imaging 2001: Image Processing. SPIE Publications, 3 July 2001. pp. 1609–1620.

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