5th Intensive Course on Soil Micromorphology Naples 2001

1. 5th Intensive Course on Soil Micromorphology Naples 2001 12th - 14th September Image Analysis Lecture 2 Image Acquisition Historic Aspects

2. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Image acquisition The four I’s of Microfabric Analysis • Image acquisition • normal photographs (via scanner) • optical microscope (via digital camera) • electron microscope (directly via A/D converter) • Image Processing • Image enhancement • Filtering • Image reconstruction • Image Analysis • Quantitative analysis • Interpretation

3. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Image acquisition • Image Acquisition: - Requirements • Spatial Resolution • Intensity resolution • Illumination issues • Image distortion • Image formats

4. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Image acquisition • 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.

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

6. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Image acquisition • 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. Spatial Resolution:- Digital Recording • 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]

7. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Image acquisition • Scanners: • The resolution on these may be adjusted • Often set at default values between 50 and 200 dpi • options often up to 1200 dpi Spatial Resolution:- Digital Recording 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 pixels Each 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.

8. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Image acquisition 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 levels • 0 - 255 grey levels • 0 - 65535 or higher • False Colour: • 0 - 255 pseudo colours • TrueColour: • 16+ million colour shades

9. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Image acquisition Intensity resolution 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.

10. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Image acquisition Intensity resolution Storage values for 512 x 512 image • 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

11. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Image acquisition Intensity resolution • 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)

12. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Image acquisition 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.

13. full 0 - 255 range saturated above 150 Saturated above 200 saturated above 150 and below 50 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Image acquisition Illumination issues Though (b) or (c) may look better, (a) contains more information

14. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Image acquisition Illumination issues full 0 - 255 range Over-saturated Some image acquisitions systems when using byte (0 - 255) range - reflect range when saturation occurs. 256 >>> 0, 257 >>> 1etc. - see effect in bright areas

15. 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

16. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Image acquisition Image Distortion Optics of microscope can distort image >>> problems with measurement

17. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Image acquisition Image Distortion Microscope should be calibrated with a grid

18. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Image acquisition 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

19. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Image acquisition 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

20. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Historic Aspects Historic Development of Image Quantification Optical Methods • Optical Diffraction was used as a method to assess orientation in 1970s. • Related technique of Convolution Square was also used

21. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Historic Aspects Historic Development of Image Quantification Upturned plates on sand grain The diffraction pattern indicates preferred orientation direction, degree of orientation and spacing of features

22. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Historic Aspects Historic Development of Image Quantification A high degree of orientation in consolidated clay shown by shape of diffraction pattern. Note: inverse spacing relationship between diffraction pattern and image

23. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Historic Aspects Digital equivalent of Optical Diffraction • The Optical Diffraction Pattern of images may be computed digitally as Fourier Transform: • - this is exploited in image reconstruction in Lecture 10

24. Image Convolution of image with itself (cross-correlation) 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Historic Aspects Digital equivalent of Convolution Note: unlike diffraction the spacing of features in convolution is directly related to spacings in image

25. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Historic Aspects 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.

26. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Historic Aspects Geometry of SEM • At low magnification • < 500 • central projection • At high magnification • > 1000x • parallel projection

27. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Historic Aspects Unconsolidated Kaolin - picture width = 6.2 m

28. 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Historic Aspects Stereo-photogrammetry Stereo photograph and associated Pole Diagram showing preferred 3 - D orientation