5th Intensive Course on Soil Micromorphology Naples th - 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 Is of Microfabric Analysis Image Processing Image enhancement Filtering Image reconstruction Image Analysis Quantitative analysis Interpretation 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 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. 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 mm ( ~ x1000 in the SEM). Digital recording medium resolution 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. 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 pixels Ideally, for high quality analysis 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] 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Image acquisition Spatial Resolution:- Digital Recording

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

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

Intensity resolution 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 [must be integer values] INTEGER: grey levels [2 bytes per pixel] >> 512 kBytes range [must be integer values] REAL: Higher grey level resolutions [REAL format] storing as 4 bytes per pixel >> 1024 kBytes minimum intensity -1 x : maximum 1 x Storage values for 512 x 512 image 5th Intensive Course on Soil Micromorphology - Naples 2001 Image Analysis - Lecture 2 Image acquisition

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 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)

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.

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

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

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 Normal Image Centralised Illumination Gradation from top left

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

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

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 ( ) 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

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

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

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

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

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.

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

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

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