Index

2D gels

Image registration | Enhance spots

3D

Frame Controls | Frame Controls

custom format: Custom image format examples

3D images

UNIX-specific error messages

3d plot

3D Plot

__register_frame_info

about menu

About menu

acknowledgments

Trademark disclaimers and acknowledgments

acquire

Scanner

Adding new fonts

Special characters | Creating new fonts

affine transform

AFM

Selecting and copying text | Repair, Backup and Restore

alpha channel

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

Area selection mode

arrows

Line/Arrow

ASCII

ASCII images

ATI

Windows and OS/2 compatibility | Problems

atomic force microscopes

Automatic Background Calculation

automatic background correction

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

Repair, Backup and Restore

backing up images

Barney the dinosaur

exploding heads: Copy/Move

barrel distortion

removing: Removing barrel or pincushion

batch mode

Erasing

Bio-Rad scanner files

bitmap editor

Spreadsheet

BMP

boxes

Box

brightness

Change colors | Brightness | Contrast | Change Gray Values

BSODs

Problems

bttv driver

Limitations and known bugs

bug reports

Submitting bug reports

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

changing computers

Tutorial on image registration

Chernobyl

Chinese

Opening images

chromakey

Paste | Chromakey

chromatic aberration

2-D Warping | 2-D Warping | Chromatic Aberration

chunkiness

reducing: Pixel interact mode

circles

Circles, ellipses, and rounded

closing

clustering

fuzzy: Automatic Background Calculation | Fuzzy Partitioning

CMYK

color

converting from grayscale: Color and Gray scale
reduction: Opening images
settings: Configure...

color menu

Color menu

color planes

Summary of macro commands

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

commands

command line interface: Summary of macro commands | Erasing

compiling

Creating Composite Images

general instructions: General compiling instructions
in Cygwin: Installation on Cygwin Xfree
in FreeBSD: Installation on FreeBSD
in Irix: Installation on SGI Irix
in Max OSX: Installation on Mac OSX
in Open VMS: Installation in OpenVMS
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

compression

Reading unusual image files | Save image

configure menu

Configure menu

confocal microscope

Mathematical pixel operations (Image | Predefined Variables

constants

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

convolution

fft: Fourier Transform
wavelet: Filtering and convolution using

copy

Copy/Move

creating image

from selected area: Creating Composite Images

Creating new fonts

Creating new fonts

crop

Crop

CT images

Reading CT, X-ray, or

cursor

curves

B-spline: B-spline curve
Bezier: Bezier curve

custom format

3D: Custom image format examples

custom image format

Create file format

customization

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

Automatic Background Calculation

deleting region

Delete region

densitometry

automatic

Spot Densitometry

automatic background

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

Installation instructions

directories, recommended

DOS commands

Custom image format examples

double-clicking

Automatically selecting objects

draw menu

Draw menu

edge detection

Circles, ellipses, and rounded

ellipses

Enhance spots

Enhance spots

erase image

erasing

Spray | Erasing

erasing background

Erase background

erosion

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

error messages

all versions: Error messages
DOS/Windows: DOS/Windows-specific error messages
UNIX: UNIX-specific error messages

evaluating expressions

Evaluating expressions

exploding heads

Copy/Move

expressions

evaluating: Evaluating expressions
image names: Using image names as

false colors

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

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

FFT used in: Digital Filtering of images
morphological: Morphological analysis
spray: Spray
using wavelets: Filtering and convolution using
wavelet: Filtering and convolution using

FITS

fixed point warping

flipping images

Rotating

floating magnifier

Floating Magnifier

flood fill

Flood Fill

fonts

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

for loops

Using ``scissors'' to manually

formulas

user-defined: Mathematical pixel operations (Image

fractal

frame rate test

General compiling instructions | Problems with Freetype

FreeBSD

installation: Installation on FreeBSD | Installation on FreeBSD

Freetype

freetype labels

Freetype labels

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

gradient

Add/Remove Gradient

grain counting

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

comparison of algorithms: Grain counting and pattern

grayscale

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

Greek text

Special characters

gunzip

gzip

Save image

Hauppauge WinTV camera

HAVE_LEX

help

files: Installation instructions

help menu

Mathematical pixel operations (Image

histogram

Histogram

histogram equalization

Histogram equalization

image

closing: Custom image format examples
reading: Open image
repairing: Miscellaneous features
selecting: Select image

image algebra

image analysis terms

image menu

Image menu

image names

Using image names as

image notes

image properties

Image properties

image registration

image types

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

input

installation

Installation instructions | Compiling

intensity

Change colors | Change Gray Values

pixel: Image Analysis Terms

Irix

installation: Installation on SGI Irix

JPEG

Save image

keycodes

L^ATEXcommands

labels

Labels

Laplace filter

Leaning Tower of Pisa

2-D Warping

lex

libpng

Problems with libpng

libtiff

Evaluating expressions | Loops and control structures

license

GPL: Usage license

lines

Line/Arrow

least-squares: Least-squares line

loops

low frequencies

removal: Filter

luminosity

Color and Gray scale

Lumisys

LZW

Miscellaneous notes

Macintosh

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
crop: 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

floating: Floating Magnifier

maps

contour: Quick Segmentation

masks

Mask

math

pixel: Mathematical pixel operations (Image
spraying: Spray

mattes

Paste

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

mouse

Basic image manipulation

problems: Problems

move

Copy/Move

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

crashing: Limitations and known bugs

neural networks

NMR images

Reading CT, X-ray, or

noise filter

Repair, Backup and Restore | Repair, Backup and Restore

non-rectangular regions

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

Open VMS

installation: Installation in OpenVMS

opening

options

command-line

dos: DOS command-line options
unix: Unix Command-line options

OS/2

paint region

Paint Region

painting

interaction with selected objects: Using ``scissors'' to manually

palette

panel

partitioning

paste

pattern counting

pattern recognition

Enhance spots

patterns

Set foreground pattern

PCL

PCX

PDS

peak areas

performance

PET scan images

displaying as panel: Multi-frame Images

PET scanner

pincushion distortion

removing: Removing barrel or pincushion

pixel density

pixel interaction mode

Pixel interact mode

pixel value

changing: Change pixel value

plugins

creating: Creating, executing, and testing
scanner: Creating, executing, and testing

polygons

Polygon

Post processing

posterized

Problems | Problems

PostScript

predefined variables

Predefined Variables

printer

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

printing to stdout

problems

Problems

process menu

psychiatrist

M-x not working: Problems
when needed: Problems

quantization

Opening images

quick segmentation

QuickCam

rank leveling

raw bytes

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

Readhdf

reading mail

Erasing

Readtif

Deconvolution and image reconstruction

reconstruction of images

rectangular areas

selecting: Selecting rectangular areas

registration

Unix Command-line options

tutorial: Tutorial on image registration

remapping colors

Remap colors

remote execution

remove low frequencies

repeat previous command

resizing

Change size

resources

Motif: X Window Resources
non-Motif: Non-Motif Resources

RGB planes

separating: Separate colors

root window

root-permanent

Circles, ellipses, and rounded

rotating images

Rotating

rounded rectangles

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

Selecting rectangular areas

shift

Multi-frame Images | Measure

Shift+click

signal distribution

Grain counting and pattern | Possible problems with Grain

size distribution

skeletonization

sketch mode

Sketch

smoothing

Sobel

multiplicative: Filter

Sobel filter

Solaris

installation: Installation on Solaris 2.5

source code

Usage license

sparse

Non-Motif Resources

spatial differencing

special characters

Special characters

spots, enhancing

Enhance spots

spray

Spray

erasing: Spray | Erasing
filtering: Spray
line: Spray
math: Spray

spreadsheet

Spreadsheet

stencil

Selecting and copying text | Paste

string variables

Variable Types

structuring element

subscripts

Sun workstations

superscripts

Repair, Backup and Restore

supported platforms

Usage license

switching selected/unselected regions

Targa

Features | Miscellaneous notes

tessellation

Watershed Segmentation

text

adding: Labels | Freetype labels | Special characters
copying: Selecting and copying text
selecting: Selecting and copying text

text files

Installation instructions

editing: Erasing

TIF

Miscellaneous notes

tnimage.hlp

tnimage.ini

tnimage.pif

Trademark disclaimers and acknowledgments

tnshell

Erasing

tracing curves

Trace curve

trademarks

transparency

trapezoid

tutorial files

undo

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

warping

fixed point: Image registration

warping images

Warp

warping, 2D

2-D Warping

warranty

Usage license

See also exploding heads: Copy/Move

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

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

Custom image format examples

X-ray images

Reading CT, X-ray, or

X-ray scanner

Xbae