Index

.Xdefaults file

X Window Resources

2D gels

Image registration

3D

Frame Controls | Frame Controls

custom format

Custom image format examples

3D images

Reading unusual image files

3d plot

3D Plot

__register_frame_info

UNIX-specific error messages

about menu

About menu

acknowledgments

Trademark disclaimers and acknowledgments

acquire

Scanner

affine transform

Image registration

AFM

Reading unusual image files

alpha channel

Selecting and copying text | Repair, Backup and Restore

animated images

Reading unusual image files | Save image | Multi-frame Images

creating

Multi-frame Images

area

measurement

Area Measurement

area measurements

Obtaining the most accurate

arrows

Line/Arrow

ASCII

Features

ASCII images

Reading unusual image files

ATI

Windows and OS/2 compatibility | Problems

atomic force microscopes

Reading unusual image files

automatic background correction

Automatic Background Calculation

background

Basic image manipulation

display

Miscellaneous features

flattening

Filter

force to fixed value

Filter

rank leveling

Filter

remove low frequencies

Filter

subtracting

Filter

unsharp mask

Filter

background flatten

Filter | Filter

background subtraction

Filter

backing up images

Repair, Backup and Restore

Barney the dinosaur

exploding heads

Image menu

batch mode

Erasing

bitmap editor

Spreadsheet

BMP

Features

boxes

Box

brightness

Change colors | Brightness | Contrast | Change Gray Values

BSODs

Problems

bttv driver

Camera Interface

bug reports

Submitting bug reports

bugs

Limitations and known bugs

buttons

User-Defined Custom Buttons

byte order

Installation on SGI Irix | If you have problems | Non-Motif Resources | Opening images | Reading CT, X-ray, or

calibrating

Calibrate

calibration coefficients

Calibrate

camera

Camera Interface

changing computers

Windows and OS/2 compatibility

Chernobyl

Tutorial on image registration

Chinese

Opening images

chromakey

Image menu | Chromakey

chunkiness

reducing

Pixel interact mode

circles

Circle

closing

Morphological analysis

clustering

fuzzy

Automatic Background Calculation | Fuzzy Partitioning

CMYK

Features | Opening images | Opening images | Save image | Print | Print

color

converting from grayscale

Color and Gray scale

reduction

Opening images

settings

Configure...

color menu

Color menu

color planes

Configure...

colormaps

Opening images | Color menu | Configure...

changing

Change colormap / false-color

reading from disk

Change colormap / false-color

remapping

Change colormap / false-color

rotating

Change colormap / false-color

sorting

Change colormap / false-color

colors

remapping

Remap colors

comma

Non-Motif Resources

command-line

Summary of macro commands

commands

command line interface

Summary of macro commands | Erasing

compiling

Compiling

general instructions

General compiling instructions

in Cygwin

Installation on Cygwin Xfree

in Irix

Installation on SGI Irix

in Max OSX

Installation on Mac OSX

on DEC Alpha

Installation on DEC Alpha

on Solaris

Installation on Solaris 2.5

problems

If you have problems

solutions

If you have problems

with Lesstif

Compiling with Lesstif

composite image

from list of coordinates

Creating Composite Images

composite images

Creating Composite Images

compression

Reading unusual image files | Save image

configure menu

Configure menu

confocal microscope

Reading unusual image files

constants

Mathematical pixel operations (Image | Predefined Variables

COMPENSATE

Mathematical pixel operations (Image | Predefined Variables | Macro Command Reference | Macro Command Reference

INVERT

Mathematical pixel operations (Image | Predefined Variables | Macro Command Reference | Macro Command Reference

contour maps

Quick Segmentation | Pixel interact mode

contrast

local

Filter

maximizing

Contrast

control structures

Loops and control structures

convolution

fft

Fourier Transform

wavelet

Filtering and convolution using

copy

Image menu

creating image

from selected area

Creating Composite Images

CT images

Reading CT, X-ray, or

cursor

Configure...

curves

B-spline

B-spline curve

Bezier

Bezier curve

custom format

3D

Custom image format examples

custom image format

Create file format

customization

X Window Resources

Motif widgets

X Window Resources

non-Motif resources

Non-Motif Resources

user-defined buttons

User-Defined Custom Buttons

Cygwin

installation

Installation on Cygwin Xfree

Darwin

installation

Installation on Mac OSX

de-trending

Filter | Filter

decimal points

Non-Motif Resources

deconvolution

fft

Fourier Transform

problems

Problems

definitions

Image Analysis Terms

densitometry

automatic

Spot Densitometry

automatic background

Automatic Background Calculation

best area selection method

Spot Densitometry

Curve

Curve Densitometry

fixed size rectangular

Manual

irregular shape

Manual

lists of spots

Spot densitometry using lists

manual rectangular

Manual

obtaining accurate measurements

Obtaining the most accurate

peak areas

Peak Areas

plotting results

Plotting densitometry results and

spot

Spot Densitometry

strip

Strip Densitometry

procedure

Strip densitometry procedure

depth

changing

Change color depth

differencing

spatial

Grain counting and pattern

Digital

installation

Installation on DEC Alpha

dilation

Morphological analysis

directories, recommended

Installation instructions

DOS commands

Custom image format examples

double-clicking

Automatically selecting objects

draw menu

Draw menu

edge detection

Filter

erase image

Miscellaneous features

erasing

Spray | Erasing

erosion

Morphological analysis

error messages

all versions

Error messages

DOS/Windows

DOS/Windows-specific error messages

UNIX

UNIX-specific error messages

evaluating expressions

Evaluating expressions

exploding heads

Image menu

expressions

evaluating

Evaluating expressions

image names

Using image names as

false colors

Change colormap / false-color | Change colormap / false-color

features

Summary of features in

different versions

Summary of features in

summary

Features

FFT

Fourier Transform

copying into image

Digital Filtering of images

digital filtering

Digital Filtering of images

erasing

Digital Filtering of images

opening

Digital Filtering of images

saving

Digital Filtering of images

file formats

image registration

File formats for landmark

file output

Input and output

fill region

Flood Fill

gradient

Add/Remove Gradient

filter

Adaptive maximize local contrast

Filter

background flattening

Filter

background subtract

Filter

engrave

Filter

force background to fixed value

Filter

high-pass

Filter

Laplace

Filter

low-pass

Filter

Maximize local contrast

Filter

multiplicative Sobel

Filter

noise

Filter

rank leveling

Filter

remove low frequencies

Filter

sharpen

Filter

Sobel

Filter

spatial differencing

Filter

unsharp mask

Filter

user-defined

Filter

filtering

Filter

FFT used in

Digital Filtering of images

morphological

Morphological analysis

spray

Spray

using wavelets

Filtering and convolution using

wavelet

Filtering and convolution using

FITS

Features

fixed point warping

Image registration

flipping images

Rotating

floating magnifier

Floating Magnifier

flood fill

Flood Fill

fonts

Non-Motif Resources | Subscripts and fonts: Embedded | Text Font

for loops

Loops and control structures

formulas

user-defined

Mathematical pixel operations (Image

fractal

Using ``scissors'' to manually

frame rate test

Miscellaneous features

frequently asked questions

Frequently asked questions

function variables

Variable Types

fuzzy k-means

Automatic Background Calculation | Fuzzy Partitioning

gamma correction

Image Analysis Terms | Calibrate

gamma table

Show O.D. table

changing

Show O.D. table

Gates, Bill

See also Windows

Problems

GIF

Features | Problems

goto

Loops and control structures

gradient

Add/Remove Gradient

grain counting

Grain counting and pattern

comparison of algorithms

Grain counting and pattern

grayscale

Change colormap / false-color | Change colormap / false-color

converting to

Save image | Color and Gray scale

images

Features | Image Analysis Terms

intensity mapping

Grayscale intensity mapping

problems viewing

Problems

remapping gray levels

Reading CT, X-ray, or

warning about changing depth of

Change color depth

Greek letters

Subscripts and fonts: Embedded

gunzip

Reading unusual image files

gzip

Save image

Hauppauge WinTV camera

Camera Interface

HAVE_LEX

Compiling

help

files

Installation instructions

help menu

Miscellaneous features

histogram

Histogram

histogram equalization

Histogram equalization

image

closing

Custom image format examples

reading

Open image

repairing

Miscellaneous features

selecting

Select image

image algebra

Mathematical pixel operations (Image

image analysis terms

Image Analysis Terms

image menu

Image menu

image names

Using image names as

image notes

Miscellaneous features

image properties

Image properties

image registration

Image registration

image types

Image Analysis Terms

images

grayscale

Image Analysis Terms | Grayscale intensity mapping

indexed-color

Image Analysis Terms

moving

Basic image manipulation

multi-frame

Multi-frame Images | Multi-frame Images | Measure

printing

Print

saving to disk

Save image

scanning

Scanner

unknown type

Reading CT, X-ray, or

windows

Image windows

IMG

Features

input

Input and output

installation

Installation instructions | Compiling

intensity

Change colors | Change Gray Values

pixel

Image Analysis Terms

Irix

installation

Installation on SGI Irix

JPEG

Save image

keycodes

X Window Resources

L^ATEXcommands

Subscripts and fonts: Embedded

labels

Text

Laplace filter

Filter

Leaning Tower of Pisa

Warp

lex

Compiling

libtiff

Creating, executing, and testing

license

GPL

Usage license

lines

Line/Arrow

least-squares

Least-squares line

loops

Evaluating expressions | Loops and control structures

low frequencies

removal

Filter

luminosity

Color and Gray scale

Lumisys

Features

LZW

Miscellaneous notes

Macintosh

Reading unusual image files

macro commands

automaticundo

Macro Command Reference

backgroundcolor

Macro Command Reference

bcolor

Macro Command Reference

between

Macro Command Reference

brightness

Macro Command Reference

cdensity

Macro Command Reference

changepalette

Macro Command Reference

changepixelvalues

Macro Command Reference

changesize

Macro Command Reference

color

Macro Command Reference

compositergb

Macro Command Reference

contrast

Macro Command Reference

convert

Macro Command Reference

darken

Macro Command Reference

densitometry

Macro Command Reference

down

Macro Command Reference

drawcircle

Macro Command Reference

drawfilledrectangle

Macro Command Reference

drawlabel

Macro Command Reference

drawline

Macro Command Reference

drawrectangle

Macro Command Reference

duplicate

Macro Command Reference

evaluate

Macro Command Reference

exit

Macro Command Reference

fclose

Macro Command Reference

fcolor

Macro Command Reference

fft

Macro Command Reference

fftdisplay

Macro Command Reference

fileformat

Macro Command Reference

filter

Macro Command Reference

findspots

Macro Command Reference

fopen

Macro Command Reference

for

Macro Command Reference

foregroundcolor

Macro Command Reference

frame

Macro Command Reference

getstring

Macro Command Reference

goto

Macro Command Reference

input

Macro Command Reference

intensity

Macro Command Reference

invertcolors

Macro Command Reference

left

Macro Command Reference

lighten

Macro Command Reference

load

Macro Command Reference

loadfft

Macro Command Reference

localcontrast

Macro Command Reference

mask

Macro Command Reference

max

Macro Command Reference

maximize

Macro Command Reference

message

Macro Command Reference

messages

Macro Command Reference

min

Macro Command Reference

move

Macro Command Reference

moveto

Macro Command Reference

movie

Macro Command Reference

new

Macro Command Reference

open

Macro Command Reference

other commands

Summary of macro commands

palette

Macro Command Reference

pasteimage

Macro Command Reference

pixel_interact_mode

Macro Command Reference

pixels

Macro Command Reference

plugin

Macro Command Reference

pow

Macro Command Reference

print

Macro Command Reference

rdensity

Macro Command Reference

resize

Macro Command Reference

right

Macro Command Reference

rotate

Macro Command Reference

save

Macro Command Reference

select

Macro Command Reference

selectimage

Macro Command Reference

separatergb

Macro Command Reference

setbackgroundcolor

Macro Command Reference

setcolor

Macro Command Reference

setpixel

Macro Command Reference

shift

Macro Command Reference

shift-enter

Macro Command Reference

spotsignal

Macro Command Reference

spotsize

Macro Command Reference

spotx

Macro Command Reference

spoty

Macro Command Reference

spray

Macro Command Reference

step

Macro Command Reference

stop

Macro Command Reference

testplugin

Macro Command Reference

threshold

Macro Command Reference

title

Macro Command Reference

transparency

Macro Command Reference

unsetpixel

Macro Command Reference

up

Macro Command Reference

wantimagetitle

Macro Command Reference

while

Macro Command Reference

windowborder

Macro Command Reference

windows

Macro Command Reference

write

Macro Command Reference

macro programming guide

Macro Programming Guide

macros

Summary of macro commands | Erasing

magnify

Magnify

floating

Floating Magnifier

maps

contour

Quick Segmentation

masks

Mask

math

pixel

Mathematical pixel operations (Image

spraying

Spray

mattes

Image menu

Max OSX

installation

Installation on Mac OSX

measurement

area

Area Measurement

measuring

angles

Measure

curves

Measure

distances

Measure

memory

insufficient

Problems | Problems

low

Operating under low-memory conditions

virtual

Windows and OS/2 compatibility

menu bars

Menu Bars

molecular weight

Calibrate

Morphological analysis

Morphological analysis

mouse

Basic image manipulation

problems

Problems

move

Image menu

movies

Multi-frame Images | Frame Controls | Frame Controls | Measure

MRI images

displaying as panel

Multi-frame Images

multi-frame images

Reading unusual image files | Save image

Netscape

X Window Resources

crashing

Limitations and known bugs

neural networks

Grain counting and pattern

NMR images

Reading CT, X-ray, or

noise filter

Filter

non-rectangular regions

Repair, Backup and Restore | Repair, Backup and Restore

notes

image

Miscellaneous features

numeric variables

Variable Types

Nyquist

Fourier Transform

O.D. table

Show O.D. table

changing

Show O.D. table

objects

selecting

Automatically selecting objects | Using ``scissors'' to manually

open image

Open image

opening

Morphological analysis

options

command-line

dos

DOS command-line options

unix

Unix Command-line options

OS/2

Windows and OS/2 compatibility

paint region

Paint Region

painting

interaction with selected objects

Using ``scissors'' to manually

palette

Color menu

panel

Multi-frame Images

partitioning

Fuzzy Partitioning

paste

Image menu

pattern counting

Grain counting and pattern

patterns

Set foreground pattern

PCL

Print

PCX

Features

PDS

Features

peak areas

Peak Areas

performance

Problems

PET scan images

displaying as panel

Multi-frame Images

PET scanner

Reading unusual image files

pixel density

Image Analysis Terms

pixel interaction mode

Pixel interact mode

pixel value

Image Analysis Terms

changing

Change pixel value

plugins

Creating, executing, and testing

creating

Creating, executing, and testing

scanner

Creating, executing, and testing

polygons

Polygon

Post processing

Camera Interface

posterized

Problems | Problems

PostScript

Print

predefined variables

Predefined Variables

printer

Print

PCL

Print

printers

PostScript

Print

printing

CMY

Print

CMYK

Print | Print

color

Print

grayscale

Print

in Windows

Print

problems

Problems

RGB

Print

Tektronix printers

Print

to file

Print

under Unix

Print

printing messages

Input and output

printing to stdout

Input and output

problems

Problems

process menu

Filter

psychiatrist

M-x not working

Problems

when needed

Problems

quantization

Opening images

quick segmentation

Grain counting and pattern

QuickCam

Camera Interface

rank leveling

Filter

raw bytes

Features | Opening images | Opening images | Reading CT, X-ray, or | Custom image format examples

Readhdf

Creating, executing, and testing

reading mail

Erasing

Readtif

Creating, executing, and testing

reconstruction of images

Deconvolution and image reconstruction

rectangular areas

selecting

Selecting rectangular areas

registration

Image registration

tutorial

Tutorial on image registration

remapping colors

Remap colors

remote execution

Unix Command-line options

remove low frequencies

Filter

repeat previous command

Miscellaneous features

resizing

Change size

resources

Motif

X Window Resources

non-Motif

Non-Motif Resources

RGB planes

separating

Separate colors

root window

Miscellaneous features

root-permanent

Miscellaneous features

rotating images

Rotating

ruler

Line/Arrow

save image

Save image

scanner

configuration

Scanner

HP

Scanner

scissors

Using ``scissors'' to manually

SCSI

Scanner | Scanner

sea slugs

Chromakey

segmentation

quick

Grain counting and pattern | Quick Segmentation

watershed

Watershed Segmentation

selecting

objects

Automatically selecting objects | Using ``scissors'' to manually

text

Selecting and copying text

sharpening

Filter

shift

Multi-frame Images | Measure

Shift+click

Selecting rectangular areas

signal distribution

Grain counting and pattern

size distribution

Grain counting and pattern | Possible problems with Grain

skeletonization

Morphological analysis

sketch mode

Sketch

smoothing

Filter

Sobel

multiplicative

Filter

Sobel filter

Filter

Solaris

Configure...

installation

Installation on Solaris 2.5

source code

Usage license

sparse

Non-Motif Resources

spatial differencing

Grain counting and pattern

spray

Spray

erasing

Spray | Erasing

filtering

Spray

line

Spray

math

Spray

spreadsheet

Spreadsheet

stencil

Selecting and copying text | Image menu

string variables

Variable Types

structuring element

Morphological analysis

subscripts

Subscripts and fonts: Embedded

Sun workstations

Configure...

superscripts

Subscripts and fonts: Embedded

supported platforms

Usage license

switching selected/unselected regions

Repair, Backup and Restore

Targa

Features | Miscellaneous notes

tessellation

Watershed Segmentation

text

adding

Text

copying

Selecting and copying text

selecting

Selecting and copying text

text files

Reading unusual image files

editing

Erasing

TIF

Miscellaneous notes

tnimage.hlp

Installation instructions

tnimage.ini

Windows and OS/2 compatibility

tnimage.pif

Windows and OS/2 compatibility

tnshell

Erasing

tracing curves

Trace curve

trademarks

Trademark disclaimers and acknowledgments

transparency

Image properties

trapezoid

Trapezoid

tutorial files

Menu Bars

undo

Configure...

variables

Mathematical pixel operations (Image

function

Variable Types

numeric

Variable Types

predefined

Predefined Variables

string

Variable Types

Visible Human

Automatically selecting objects

vnc

UNIX-specific error messages

wallpaper

Miscellaneous features

warping

fixed point

Image registration

warping images

Warp

warranty

Usage license

See also exploding heads

Image menu

wavelet

Wavelet transform

convolution

Filtering and convolution using

copying into image

Copying Wavelets into an

file format

File format for wavelet-transformed

file format for functions

Wavelet file format

filtering

Filtering and convolution using | Filtering and convolution using

selecting

Selecting a wavelet

while loops

Loops and control structures

widgets

customizing

X Window Resources

Windows

Print | Windows and OS/2 compatibility

blue screen of death

Problems

crashing

Operating under low-memory conditions | Windows and OS/2 compatibility

mouse not working

Windows and OS/2 compatibility | Problems

other problems

Miscellaneous features | Windows and OS/2 compatibility | Windows and OS/2 compatibility | Problems | Problems | Problems | Problems | Problems | Problems | DOS/Windows-specific error messages

running Unix version on

Installation on Cygwin Xfree | Notes on DOS version

wireframe

3D Plot

X resources

X Window Resources

X-ray images

Reading CT, X-ray, or

X-ray scanner

Custom image format examples

Xbae

Compiling

zooming

Zoom