5th Intensive Course on Soil Micromorphology

Naples 2001

12th - 14th September

Image Analysis

Lecture 9

Grey-Level Morphology and Multi-Spectral

Methods

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Grey-Level Morphology

Multi-Spectral Methods for Segmentation/Classification

useful where X-ray spectra of different colour information (e.g. RED/GREEN/BLUE/ U-V) information is available

Part 1

Part 2

Extension of Binary Morphology to Grey-Level Images

avoids need to segment images

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Grey-Level Morphology

•Segmentation (usually by thresholding) and attendant problems

•Erosion involves stripping pixels from edge of foreground areas according to selected criteria

•Dilation involves adding pixels to foreground areas

•Opening involves one cycle of erosion followed by one cycle or dilation

roughness aspects of feature are not recovered, no are particles smaller than 2 pixels

•Closing is the reverse of Opening.

Binary Morphology requires

Grey Level Morphology

• attempts to solve problems of BINARY MORPHOLOGY

by removing need for thresholding

• Grey Level Erosion replaces all intensities within a given

mask area by the minimum value in that area

• Grey Level Dilation replaces all intensities within a given

mask area by the maximum value in that area

• A grey level opening involves an erosion and a dilation phase

As with binary morphology, roughness is lost and features tend to become rounded until they finally disappear

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Grey-Level Morphology

Representation of binary morphology for feature sizing

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Grey-Level Morphology

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Grey-Level Morphology

Schematic of Intensity Profile along a line

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Grey-Level Morphology

Start of Erosion along line

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Grey-Level Morphology

Intensity lost after grey-level erosion (blue)

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Grey-Level Morphology

Intensity lost after grey-level erosion followed by dilation

Blue: Intensity lost: Green: Intensity recovered in dilation

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Grey-Level Morphology

Intensity lost after grey-level erosion of diameter 5

Cyan: New Intensity lost

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Grey-Level Morphology

Intensity lost after grey-level erosion followed by dilation(diameter 5)

Blue/ Cyan: Intensity lost: Green: Intensity recovered in dilation

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Grey-Level Morphology

Intensity lost after grey-level erosion of diameter 7

Purple: New Intensity lost

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Grey-Level Morphology

Intensity lost after grey-level erosion followed by dilation(diameter 7)

Blue/ Cyan/Purple: Intensity lost: Green: Intensity recovered in dilation

Effect of grey-levelopening at different radii

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Grey-Level Morphology

a) Radius 9 pixels

b) Radius 10 pixels

c) Difference Image

d) Complete particle loss

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Grey-Level Morphology

Particle size analysis using grey-level morphology

1

2

3

4

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Grey-Level Morphology

Core sample taken from estuary model.

[photograph courtesy of J.Alexander]

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Grey-Level Morphology

Halimeda needles from Great Barrier Reef

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Grey-Level Morphology

Halimeda needles from Great Barrier Reef

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Grey-Level Morphology

Halimeda needles from Great Barrier Reef - partly covered by nanograins

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Grey-Level Morphology

Halimeda needles from Great Barrier Reef - partly covered by nanograins

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Grey-Level Morphology

Halimeda needles from Great Barrier Reef - fully covered by nanograins

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Grey-Level Morphology

Question: Are nanograins biological or chemical in origin?

Evidence suggests nanograins increase in size with coverage - hence favouring chemical argument.

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Grey-Level Morphology

If particles lost at each radius are stored and finally added (B) - the resulting image should be comparable to original (A).

Except: All particles are reduced to their equivalent circular

diameter.

•Allows alternative methods for segmentation

•Enables separation of different mineral classes.

•Can be used in combination with Orientation Analysis as a combination method to overcome problem of large particles

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Multi-Spectral Analysis

Requirements:

Two or more images of same area at same magnification and pixel resolution and in exact registry.

Must be collected with different physical parameters - e.g. wavelength

Multi-Spectral Analysis

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Multi-Spectral Analysis

Examples:

Optical Microscopy:

•Red / Green / Blue images

•UV.

Electron Microscopy:

•Secondary Electron

•Back Scattered Electron

•Cathodoluminescence

•X-Ray Maps.

Requirements continued:

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Multi-Spectral Methods

Require 2 or more different images of same area

must be in exact registry

e.g. Optical Microscope

RED/GREEN/BLUE/UV

Or SE / BSE Image and CL or various X - Ray Maps in SEM

Multi-Spectral Methods

Hong Kong Marine Clay from M1 unit approximately 1m above upper most palaeo-desiccated layer. BSE Image

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Multi-Spectral Methods

Hong Kong Marine Clay

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Multi-Spectral Methods

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Multi-Spectral Methods

BSE Image X-Ray Maps

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Multi-Spectral Methods

From N images

and

Statistics from M classes

Output segmented image may be obtained.

Accuracy in segmentation relies on identification of suitable classes, and also sufficient classes

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Multi-Spectral Methods

Are these two particles the same material?Classification was set at 98% confidence and some post-processing was done to produce classified image.

Procedure of segmentation is know as Mineral-Segmentation

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Multi-Spectral Methods

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Multi-Spectral Methods

large voids 2.21% matrix 73.49% matrix in aggregate 14.46% quartz 5.27% feldspar 2.70% chalk 0.64% rutile 0.15% magnetite 0.65% pyrite 0.43%

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Multi-Spectral Methods

Particle Size Distribution for different mineral species

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Multi-Spectral Methods

Binary Mask to assess orientation in matrix outside aggregate. Large mineral grains and voids are black as is aggregate.

Binary Mask to assess orientation in matrix inside aggregate.

Use Mineral Segmented image to generate binary masks.

Domain Segmentation of Matrix

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Multi-Spectral Methods

Hong Kong Marine Clay

a) Matrix orientation c) Quartz grain orientation e) Weighted Quartz grain orientation

b) Aggregate orientation

d) Feldspar orientation f) Weighted Feldspar orientation

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Multi-Spectral Methods

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Multi-Spectral Methods

Index of Anisotropy

outside aggregate: 0.229

inside aggregate: 0.374

In both cases the predominant orientation is nearly vertical.

Vertical direction in field.

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 9: Multi-Spectral Methods

When does a particle warrant separate identification from matrix?

- depends on pixel resolution/magnification.

In supervised classification it is helpful to avoid “forced” classification as this will identify features / minerals which may have been missed.

Some post-processing of image in needed following Mineral-Segmentation to remove noise etc.

Concluding Remark on Multi-spectral Analysis.