IMAGE ANALYSIS IN EARTH SCIENCESrenee.heibronner@unibas.ch, www.unibas.ch/earth/micro

LECTURES

• Applications of image analysis techniques to naturally and experimentally deformed rocks

• Quantitative analysis of crystallographic preferred orientations using Optical Orientation Imaging

•••• Introduction & pre-processing• Segmentation I & volume analysis• Segmentation II & grain size analysis• Shape analysis• Autocorrelation function

SHORT COURSE

IMAGE ANALYSIS versus IMAGE PROCESSING

image processing: image image

source: results:

IMAGE ANALYSIS versus IMAGE PROCESSING

image analysis: image number(s)

source: results:

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h(r)(%)

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y = 4.3885 + 6.8524x R= 0.98784

RADIUS

PERIPHERY

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software

NIH Image (OS9) / Scion Image (PC)

software

NIH Image (OS9) / Scion Image (PC)

NIH Image is a public domain image processing and analysis program for the Macintosh.

It was developed at the Research Services Branch (RSB) of the National Institute of Mental Health (NIMH), part of the National Institutes of Health (NIH).

A free PC version of Image, called Scion Image for Windows, is available from Scion Corporation.

There is also ImageJ, a Java program inspired by Image that "runs anywhere".

software

NIH Image (OS9) / Scion Image (PC)

BASIC FEATURES

free

widely supported

= basically mono / index color≠ RGB

macros (Pascal)

software

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NIH Image (OS9) / Scion Image (PC)

Image can acquire, display, edit, enhance, analyze and animate images. It reads and writes TIFF, PICT, PICS and MacPaint files, providing compatibility with many other applications, including programs for scanning, processing, editing, publishing and analyzing images. It supports many standard image processing functions, including contrast enhancement, density profiling, smoothing, sharpening, edge detection, median filtering, and spatial convolution with user defined kernels.

Image can be used to measure area, mean, centroid, perimeter, etc. of user defined regions of interest. It also performs automated particle analysis and provides tools for measuring path lengths and angles. Spatial calibration is supported to provide real world area and length measurements. Density calibration can be done against radiation or optical density standards using user specified units. Results can be printed, exported to text files, or copied to the Clipboard.

A tool palette supports editing of color and gray scale images, including the ability to draw lines, rectangles and text. It can flip, rotate, invert and scale selections. It supports multiple windows and 8 levels of magnification. All editing, filtering, and measurement functions operate at any level of magnification and are undoable.

software

links

THE SOFTWARE

NIH Image original for Macintosh OS9author: Wayne Rasband (source = Pascal)

Scion Image version for PC / Windows

Image SXM NIH Image adapted/expanded for OSXauthor: Steve Barrett

imageJ Java versionauthor: Wayne Rasband

links

DOWNLOADS AND INFO

NIH Image http://rsb.info.nih.gov/nih-image/

Scion Image http://www.scioncorp.com

Image SXM http://reg.ssci.liv.ac.uk/

imageJ http://rsb.info.nih.gov/ij/

on-line manual for NIH Image/Scion Image + Image SXMhttp://rsb.info.nih.gov/nih-image/manual/contents.html

macros and docus for NIH Image/Scion Image + Image SXMftp://rsbweb.nih.gov/pub/nih-image/macros/ftp://rsbweb.nih.gov/pub/nih-image/documents/

links

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NIH Image web-manual: contents.html

links

HOME PAGEDeformation and microstructure analysishttp://www.unibas.ch/earth/micro/

links

HOME PAGEDeformation and microstructure analysishttp://www.unibas.ch/earth/micro/

links

COURSE MATERIAL

http://www.unibas.ch/earth/micro/course/workshop.html

links

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introduction

FILE: open / import fileopen:formatted file(file size in header)

import:raw data file(have to set file size)

Introduction to NIH Image / Scion Image

FILE: save / export filesave:formatted file(choose format)(file name extension!)

export:raw data file(choose file type)

Introduction to NIH Image / Scion Image

FILE: get info

Introduction to NIH Image / Scion Image

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WINDOWS: LUT - Tools - Map - Info - Histogram

Windows (always open):

LUTlook-up table

Tools MapB Brightness (offset)C Contrast (slope)

InfoX,Y: LocationValue: Grey value

0 = white255 = black

Additional window:

Histogram (⌘H)no. of pixels / grey value

Introduction to NIH Image / Scion Image

EDIT: select / copy / cut / paste

Select (use selection tool or Select All (⌘A))

Copy (⌘C)

Cut (⌘X) Move Selection(use cursor or arrows)

Paste (⌘V) Draw boundary (⌘B)(draws line along active selection)

Introduction to NIH Image / Scion Image

FILE / EDIT: make grey scale

EDIT:

Select All (⌘A)

Draw Scale

PLOT PROFILE:

Tools: Select horizontal traceby pressing shift key

HISTOGRAM (⌘H)

shows 50 pixels for every grey value

FILE:

New...width = 254height = 50

Aim:create scale withall grey levels (G)

Background:theoretically:( 0 < G < 255)= 256 = 28 grey values

but 0 and 255 arereserved entries=> (256-2) grey values=> width = 254

Introduction to NIH Image / Scion Image

EDIT: scale/rotate

EDIT:

Scale and Rotate (⌘E)Interpolation method: left: bilinear (smooth) right: nearest neighbor

Introduction to NIH Image / Scion Image

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EDIT: flip horizontal/vertical - Invert

EDIT:

Scale and Rotate (⌘E)scale: 0.50rotate: 45°

EDIT:

Flip horizontal

EDIT:

Invert

Introduction to NIH Image / Scion Image

look-up tables (LUT)

LUT: use tool or option tool

MAP: use B / C

OPTION: Look-up tableLUT optionsThresholdDensity slice

PROCESS: Enhance contrastEqualize

MACRO: Lazy starter LUTs etc.

NOTE: LUT operations do not affect grey values of image

look-up tables (LUT)

input

output

Look-up Tables

0 input gray value1 grayscale = default = 1:12 System LUT3 Rainbow4 Spectrum5 Fire-1, LUT option 16grayscales

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Map / LUTTransfer curve

image is not changed

LUTs - transfer curve - contrast

look-up tables (LUT)

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look-up tables (LUT)

EDIT: open oolite400.tif

LUT: use tool or option tool

look-up tables (LUT)

MAP: use B / C

look-up tables (LUT)

OPTION: Look-up table

look-up tables (LUT)

rainbow

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OPTION: LUT options

look-up tables (LUT)

OPTION: Threshold

look-up tables (LUT)

OPTION: Density slice

look-up tables (LUT)

PROCESS: Enhance contrast

look-up tables (LUT)

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PROCESS: Equalize

look-up tables (LUT)

Lazy starter LUTs

SPECIAL: Load macro "Lazy starter LUTs”

macro 'Invert LUT [I]';var i:integer;begin for i:=1 to 254 do begin RedLUT[i]:=255-RedLut[i]; GreenLUT[i]:=255-GreenLut[i]; BlueLUT[i]:=255-BlueLut[i]; end; UpdateLUT;end;

macro 'Log Transform';var i,v:integer; scale:real;BEGIN scale := 255.0 / ln(255.0); for i:=1 to 254 DO begin v := 255-round(ln(i) * scale); RedLUT[i]:=v; GreenLUT[i]:=v; BlueLUT[i]:=v; end; UpdateLUT;END;

etc.....

macro: Lazy starter LUTs

Plot LUT [P]

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B

input (index): optical density:0 = white 255 = blackoutput: brightness:255 = white 0 = black

macro: Lazy starter LUTs

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Plot LUT [P]

R

G

B

R Y G C B M R

macro: Lazy starter LUTs

Invert LUT [I]

macro: Lazy starter LUTs

Log transform

macro: Lazy starter LUTs

Gamma transform...

macro: Lazy starter LUTs

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Square transform

macro: Lazy starter LUTs

Parabolic transform

macro: Lazy starter LUTs

Square root transform

macro: Lazy starter LUTs

Sine transform

macro: Lazy starter LUTs

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Half-sine transform

macro: Lazy starter LUTs

Posterize...

macro: Lazy starter LUTs

Colour strips

macro: Lazy starter LUTs

Make four ramp LUT

macro: Lazy starter LUTs

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Change One LUT Entry

macro: Lazy starter LUTs

Change LUT from ... to ...

macro: Lazy starter LUTs

pre-processing

1. record image

2. segment

3. analyze

4.

...not so easy...

GENERAL IDEA:

pre-processing

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1. record image

2. pre-process1. contrast

2. background

3. sharpen

4. scale

3. segment

4. analyze

scale, bckg, +yellow (-blue), sharpen

scale, bckg, sharpen

crop, scale, +yellow (-blue)

scale, +red (-cyan)

pre-processing

CONTRAST: SPECIAL 1D LUT calibration

BACKGROUND: PROCESS Subtract background- 1D horizontal- 1D vertical- 2D rolling ball- 2D remove streaks

PROCESS Image Math

SPECIAL Lazy lighting

SHARPEN: PROCESS SmoothSharpen

SCALE: ANALYZE Set scale...

pre-processing

CONTRAST: SPECIAL 1D LUT calibration

pre-processing

applyLUT

SCALE: ANALYZE Set scale...

pre-processing

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BACKGROUND: PROCESS Subtract background- 1D horizontal- 1D vertical- 2D rolling ball- 2D remove streaks

pre-processing

Lazy lighting

macro: Lazy lighting

SPECIAL: Load macro "Lazy lighting”

histogram left [A] histogram right [Z]Determine average brightness

macro: Lazy lighting

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histogram top [T] histogram bottom [B]

macro: Lazy lighting

Determine average brightness

correct top-bottom [F]Correct linear brightness trend

macro: Lazy lighting

select center [S] correct light [C]Correct radial brightness trend

macro: Lazy lighting

Results of background correction

macro: Lazy lighting

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