5th Intensive Course on Soil Micromorphology Naples 2001

5th Intensive Course on Soil Micromorphology

Naples 2001

12th - 14th September

Image Analysis

Lecture 2

Image Acquisition

Historic Aspects

• Image acquisition

• normal photographs (via scanner)• optical microscope (via digital camera)• electron microscope (directly via A/D converter)

The four I’s of Microfabric Analysis

•Image Processing• Image enhancement • Filtering• Image reconstruction

• Image Analysis

•Quantitative analysis

• Interpretation

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 2 Image acquisition

Image Acquisition: - Requirements

•Spatial Resolution

•Intensity resolution

•Illumination issues

•Image distortion

•Image formats


Image Acquisition: - Requirements

Spatial Resolution

Photographic Recording:

Photographic enlargement is possible often up to 10 times depending on grade of film.

Low magnification covers larger area, and detail can be seen with enlargement.

Digital Recording:

NOT possible to enlarge to “see” detail.

Magnification / resolution must be selected at outset.

May be a compromise between area covered and detail.


Spatial Resolution:- Digital Recording

Image divided into pixels which are the smallest element that can be resolved. Area covered by each pixel depends on the field of view and this will vary with the magnification in use.

Field of view - 0.1 mm ( ~ x1000 in the SEM).

Digital recording medium resolution - 512 x 512 pixels

>>>> each pixel will represent about 0.2 m.

Enlargement of (a) by x 4 gives no additional information.

Isolated features (c) 1 pixel wide can be resolved, but not if they touch (e).

Pixel size should be no more than ~ 50% of smallest feature.


•Most modern frame stores /cameras have a minimum resolution of around 400 - 500 pixels

•Ideally, for high quality analysis 1000 - 2000 pixel device should be used.

•One SEM manufacturer has an option of a frame store > 3000 pixels.

In the SEM

double number of pixels >>> 50% reduction in magnification

increases the area covered by a factor of 4.

[but may not be entirely true if beam diameter is adjusted with magnification]



Scanners:• The resolution on these may be adjusted• Often set at default values between 50 and 200 dpi• options often up to 1200 dpi

For a 150 x 150 mm image and 100 dpi, image is 600 x 600 pixels. Each pixel 0.25 mm

At 1200 dpi, the image will be very large at 7200 x 7200 pixelsEach pixel 0.02mm

For a black and white image (grey-level image):

storage 100 dpi >> 0.36Mbyte storage (for 150 x 150 mm image)

1200 dpi >> 50 Mbyte for a single image.



Intensity resolution

Human eye can resolve about 16 grey levels at best

Monochrome publications can achieve 8 at best.

Digital Images:

Binary image: Black and White only

pores black - solids white or vice versa

Grey Level Image:0 - 15 grey levels0 - 255 grey levels0 - 65535 or higher

False Colour: 0 - 255 pseudo colours

True Colour: 16+ million colour shades



Binary images:

Binary images are basis of much image processing e.g. particle/feature size analysis.

Each pixel is either 1 (foreground) or 0 background and may be stored in a single bit.

Data storage is usually in form of BYTES - or 8 bits.

8 pixels stored in each byte. (32 kbytes needed to store image.

Most images are not in binary form and must be converted before most image processing/analysis packages can be used.



Grey Level Images:

16 grey levels (used by older devices).

store data from 2 pixels in each byte >>128 kBytes

BYTE: 256 grey levels [most common] >> 256 kBytes

range 0 - 255 [must be integer values]

INTEGER: 65536 grey levels [2 bytes per pixel] >> 512 kBytes

range -32376 - 32375 [must be integer values]

REAL: Higher grey level resolutions [REAL format]

storing as 4 bytes per pixel >> 1024 kBytes

minimum intensity -1 x 1038 : maximum 1 x 1038

Storage values for 512 x 512 image




False Colour:

Usually equivalent to 256 grey level images:

individual grey level shades are shown by colour shades to overcome limitations of human eye.

True Colour:

Often as RGB (red: green: blue) - [most common]

each colour has an intensity range 0 - 255 giving

16+ million possible colours. 3 bytes (24 bit) are needed for each pixel

Sometimes CYM (cyan: yellow: magenta) is used

Alternatively: HSI (Hue: Saturation: Intensity)


Illumination issues

Binary Images often needed for analysis

BUT

Illumination Settings at acquisition can often bias the results

•brightness and contrast of illumination >>> saturation

•brightness and contrast setting on SEM >>> saturation

•intermediate photographic developing and printing

>>> saturation

May want high contrast (and saturation for binary images)

BUT in other cases full dynamic range should be retained.


Illumination issues

full 0 - 255 range

saturated above 150

Saturated above 200

saturated above 150

and below 50

Though (b) or (c) may look better, (a) contains more information


full 0 - 255 range

Over-saturated

Some image acquisitions systems when using byte (0 - 255) range - reflect range when saturation occurs.

256 >>> 0, 257 >>> 1 etc. - see effect in bright areas

Illumination issues


Illumination issues

Non-uniform illumination will create problems in later thresholding and analysis

Normal Image

Centralised Illumination

Gradation from top left


Image Distortion

Optics of microscope can distort image

>>> problems with measurement


Image Distortion

Microscope should be calibrated with a grid


Image Formats

BMP: TIFF: JPG: GIF ------Widespread

Some formats require key information to be stored in another file problems if associated file is removed

Most formats have key header information in file itself.

Most compact formats use BYTE (0 - 255) format

can be swapped easily between platforms

BUT INTEGER format (2 bytes) may be problematic

- swapping between PC/Macintosh/UNIX (as high and low bytes are swapped).

Even more problems if REAL/ COMPLEX format is used


Image Formats

Typical Image 512 x 512 x 8 >>>> 256 kBytes

True Colour Image 4096 x 4096 x (24bit) would occupy more than 50 Mbytes

Special Formats - (RLE)

for Binary Images and selected Classified Images arising from Image Analysis - more efficiently stored in a Run-Length-Encoded format (RLE).

Applicable for BYTE and INTEGER format if large areas have the same “intensity value” - compression up to 90+% is possible.

May need to re-expand image back to normal BYTE or INTEGER format before using for Analysis purposes.

Cannot be used on grey-level images

Historic Development of Image Quantification

Optical Diffraction was

used as a method to assess

orientation in 1970s.

Related technique of

Convolution Square was

also used

Optical Methods

5th Intensive Course on Soil Micromorphology - Naples 2001Image Analysis - Lecture 2 Historic Aspects


Upturned plates on sand grain

The diffraction pattern indicates preferred orientation direction, degree of orientation and spacing of features



A high degree of orientation in consolidated clay shown by shape of diffraction pattern.

Note: inverse spacing relationship between diffraction pattern and image


The Optical Diffraction Pattern of images may be computed digitally as Fourier Transform:

- this is exploited in image reconstruction in Lecture 10

Digital equivalent of Optical Diffraction


Digital equivalent of Convolution

Image Convolution of image with itself (cross-correlation)

Note: unlike diffraction the spacing of features in convolution is directly related to spacings in image



Stereoscopy/Photogrammetry

SEM is ideal for photogrammetric measurement using stereo-photographs

Geometry of SEM should be considered with viewer at the electron source and illumination at the electron collector - i.e. and apparent reversal of convention.

At low magnification

< 500

central projection

At high magnification

> 1000x

parallel projection

Geometry of SEM


Unconsolidated Kaolin - picture width = 6.2 m



Stereo photograph and associated Pole Diagram showing preferred 3 - D orientation

Stereo-photogrammetry

5th Intensive Course on Soil Micromorphology Naples 2001

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