Contents

Table of contents is on previous page

• Introduction
  • Summary
  • Features
    • Differences between IMAL and other programs
  • Usage license
  • Summary of features in different versions
  • Submitting bug reports
  
  
• Installation instructions
  • System requirements
  • Installation overview
  • Compiling
    • General compiling instructions
    • Installing Xbae
    • Problems with Freetype
    • Problems with libpng
    • If the above procedure doesn't work
    • Creating a semi-static version
    • If it still won't compile
  • Installation on Solaris 2.5
  • Installation on DEC Alpha
  • Installation on Mac OSX / Darwin
  • Installation on FreeBSD
  • Installation on SGI Irix
  • Installation on Cygwin Xfree
  • Installation in OpenVMS
  • Compiling with Lesstif
  • If you have problems compiling the program
  
  
• Command-line options
  • Unix Command-line options
  • DOS command-line options
  • Running DOS version
    • Notes on DOS version
  
  
• Basic operations
  • Image Analysis Terms
  • Menu Bars
  • Image windows
  • Basic image manipulation
    • Selecting rectangular areas
    • Automatically selecting objects
    • Using ``scissors'' to manually select objects or groups of objects
    • Selecting and copying text
  • Operating under low-memory conditions
  • Frequently asked questions
  • Miscellaneous notes
  
  
• Customizing IMAL
  • X Window Resources
  • Non-Motif Resources
  • User-Defined Custom Buttons
  
  
• File menu
  • Open image
    • Opening images
    • Reading CT, X-ray, or MRI images, or raw bytes
    • Reading unusual image files
  • Save image
  • Print
  • Create/Resize Image
  • Multi-frame Images
    • Creating Composite Images
  • Create file format
    • Custom image format examples
  • Scanner
  • Camera Interface
  • Creating, executing, and testing plugins
  
  
• Image menu
  • Delete region
  • Crop
  • Erase background
  • Copy/Move
  • Paste
  • Changing size
    • Change size
    • Zoom
    • Floating Magnifier
  • Rotating
  • Image properties
  • Chromakey
  • Frame Controls
  • Spreadsheet
  • Repair, Backup and Restore
  
  
• Process menu
  • Filter
  • Mask
  • Flat Field / Flat Frame Correction
  • Warp
    • 1-D Warping
    • 2-D Warping
    • Removing barrel or pincushion distortion
  • Image registration
    • Registering two images manually
  • 2D Gel Analysis
    • Method 1 - Complete gel analysis
    • Method 2 - Comparing two 2D gels (DIGE-like method)
    • Highlight Image Differences
    • File formats for landmark and data point lists
    • Tutorial on image registration
  • Measure
  • Chromatic Aberration
  • Calibrate
  • Area Measurement
  • Spot Densitometry
    • Automatic
    • Manual
    • Automatic Background Calculation
    • Spot densitometry using lists of spots
    • Obtaining the most accurate densitometry measurements
    • Densitometry Measurements in Autoradiograms
  • Strip Densitometry
    • Strip densitometry procedure
    • Plotting densitometry results and other data
    • Curve Densitometry
    • Peak Areas
  • Western Blots and Stained Gels
  • Grain counting and pattern recognition
    • Comparison of Grain Counting Methods
    • Counting patterns with neural network method
    • Grain counting using neural network method
    • Grain counting using segmentation and differencing methods
    • Notes on Pattern counting
    • Grain counting tutorial
    • Grain counting example
    • Possible problems with Grain and Pattern counting
    • Data file format
    • Fuzzy Partitioning
  • Morphological analysis
  • Thresholding, Dilation, Erosion, Opening, and Closing
  • Quick Segmentation
  • Watershed Segmentation
  • Enhance spots
  • Trace curve
  • Fourier Transform
    • Deconvolution and image reconstruction
    • Digital Filtering of images using the FFT
  • Wavelet transform
    • Reconstituting an image from wavelet coefficients
    • Other options
    • Selecting a wavelet
    • Wavelet file format
    • File format for wavelet-transformed images
    • Filtering and convolution using wavelets
    • Copying Wavelets into an image
  • 3D Plot
  
  
• Color menu
  • Change colors
  • Brightness
  • Contrast
  • Change colormap / false-color
  • Grayscale intensity mapping
  • Remap colors
  • Invert colors
  • Change color depth
  • Color and Gray scale
  • Separate colors
    • Composite image
  • Histogram
  • Histogram equalization
  • Change pixel value
  • Change Gray Values
  
  
• Draw menu
  • Text
    • Ordinary labels
    • Labels
    • Drawing text at an angle
    • Freetype labels
    • Special characters
    • Creating new fonts
    • Subscripts and fonts: Embedded L^ATEX-like commands
    • Text Font
    • Pasting text
  • Set foreground color
  • Set background color
  • Set foreground pattern
  • Graphics
  • Line/Arrow
  • Flood Fill
  • Add/Remove Gradient
  • Spray
  • Circles, ellipses, and rounded rectangles
  • Other Graphic Elements
    • Add border
    • Paint Region
    • Box
    • Curve
    • Bezier curve
    • B-spline curve
    • Least-squares line
    • Polygon
    • Trapezoid
    • Snap trapezoid
    • Fixed-width rectangle
    • Open polygon
    • Sketch
    • Point to point polygon
  
  
• About menu
  • About the program
  • About the file
  • About the image
  • Select image
  
  
• Configure menu
  • Show colormap
  • Show O.D. table
    • Changing the O.D. table
  • Pixel interact mode
  • Configure...
  
  
• Mathematical pixel operations (Image Algebra)
  • Predefined Variables
  • Using image names as variables
  • Evaluating expressions
  • Input and output
  • Loops and control structures
  
  
• Summary of macro commands
  • Variable Types
  • Macro Command Reference
  • Macro Programming Guide
  
  
• Miscellaneous features
  • Erasing
  
  
• Windows and OS/2 compatibility
• Problems
  • Limitations and known bugs
  
  
• Error messages
  • All versions
  • DOS/Windows-specific error messages
  • UNIX-specific error messages
  • Trademark disclaimers and acknowledgments
  
  
• Bibliography
• Index