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5th Intensive Course on Soil Micromorphology Naples 2001

5th Intensive Course on Soil Micromorphology Naples 2001. 12th - 14th September Image Analysis. Lecture 3 Image Processing/Analysis Basic Requirements. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 3: Basic Requirements.

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5th Intensive Course on Soil Micromorphology Naples 2001

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  1. 5th Intensive Course on Soil Micromorphology Naples 2001 12th - 14th September Image Analysis Lecture 3 Image Processing/Analysis Basic Requirements

  2. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 3: Basic Requirements • Basic requirements of image processing/analysis • e.g. need to threshold or not, • problems of subjectivity, • hydrid approaches (user/computer methods). • manual methods of measurement Introduction to Sigma Scan Software

  3. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 3: Basic Requirements • Most Analysis requires some preliminary processing • Segmentation • involves separation of image into regions of similar features • simple form - 2 phases - solids and particles >> binary image • multi-phase form - may be several different discrete grey levels in an image. • More complex segementation methods may involved segmentation based on texture/morphology/orientation. • Thesholding • selection of a grey-level intensity which separates two phases. • For binary images ---------------one threshold • For multiphase images -----------several thresholds

  4. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 3 Basic Requirements Segmenting a Binary Image using Thresholding e.g. Change Grey-Level Image into 2 phases - solids and voids

  5. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 3 Basic Requirements Segmenting a Binary Image using Thresholding First Example is ideal - selection of threshold value to separate black from white Second Example: also ideal - clear definition of where threshold should be. However: Non uniform illumination may present problems.

  6. Normal Image Centralised Illumination Gradation from top left 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Image acquisition Illumination issues Non-uniform illumination will create problems in later thresholding and analysis

  7. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 3 Basic Requirements Thesholding: If intensity distribution is of simple form, and automatic threshold may be set (provided illumintaion is uniform) With grey-level images - intensity distribution often does not show a discrete minimum - making automatic thresholding difficult.

  8. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 3 Basic Requirements Thesholding: Interactive selection of threshold will be unreliable and may well differ significantly from one person to another. Data from 2nd and 3rd Intensive Courses:

  9. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 3 Basic Requirements Thesholding: Multi-phase situations A new objective method will be discussed in Lecture 10 Intensity distribution of multi-phase image. The optimum points for separation between phases are the minima

  10. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 3: Basic Requirements • Human eye is poor at intensity discrimination • computer is good at intensity discrimination • Human eye is good at texture recognition • difficult to derive suitable computer algorithms to discriminate textures. • Morphological effects - e.g. surface roughness can mask intensity effects - • e.g. quartz and felspar have similar intensities in back-scattered SEM, but the morpholoigcal appearance (texture changes in grey levels) are usually easily discriminated by human eye. Segmentation based on other methods:

  11. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 3: Basic Requirements Segmentation based on other methods: Manual delineation methods can be useful. These aim to take the advantages of the human eye in pattern recognition and define areas of equal grey-level which are the ideal for feature size analysis In this example, regions which are near vertical are coded red. There will be an exercise on this later in course

  12. BSE image of volcanic deposition: calcium map of area 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 3: Basic Requirements Sample from Monserrat Region within red area has similar grey-level, but has difference in calcium concentration. Segmentation by thresholding is not possible.

  13. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 3: Basic Requirements • Traditionally - features would be measured by laying a rule against the feature of interest. • This facility can be achieve more readily with digital images by using an overlay cursor. • Measurement requires the use of overlays these are binary images which can be overlain directly over the image without affecting the original image. • Often several different overlays are available. Sigmascan has 5 image overlays and one for annotation. Simple Measurement

  14. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 3: Basic Requirements Simple Measurement Manual Method directly on photograph Overlaying a scale. Is case, a special scale was constructed consistent with magnification. Units are in microns

  15. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 3: Basic Requirements Simple Measurement Manual Methods Interactive using a cursor. Click on one point Move cursor Click on second point Distance is automatically recorded

  16. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 3: Basic Requirements Introduction to Sigma Scan Introduction to Sigma Scan • SIGMA SCAN is a package directly available over the Internet which has a 30 day demonstration license. • Thus ideal for use in this teaching course • What does SIGMA SCAN do • allows several basic image processing procedures • limited capabilities for more advanced operation. • All quantitative work is done via the overlay planes

  17. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 3: SIGMASCAN Using SigmaScan to Threshold

  18. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 3: SIGMASCAN

  19. Use “handles” to adjust width of selected intensity values 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 3: SIGMASCAN

  20. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 3: SIGMASCAN Many of the settings for SigmaScan must be first set using this menu The next two slides show sub-options of these settings

  21. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 3: SIGMASCAN Selecting which parameters to measure

  22. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 3: SIGMASCAN Selecting which overlay to use for annotation

  23. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 3: SIGMASCAN Using MEASURE OBJECTS labels each object with an unique identifier

  24. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 3: SIGMASCAN Each Feature is measured according to parameters selected and displayed in an EXCEL Worksheet

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