Index

A

• Angle tool
  • about / Basic selections – lines, length, and profiles
• Anonymize IJ DICOM
  • URL / Study anonymization
• Apache Commons Math library
  • URL / Using external libraries
• Application Programming Interface (API)
  • URL / ImageJ plugins
• Auto Local Threshold plugin
  • URL / Auto Threshold and Auto Local Threshold
• Auto Threshold
  • URL / Auto Threshold and Auto Local Threshold

B

• batch mode
  • about / The batch mode
• BinaryProcessor object / A sample plugin
• BMP / Opening images with a certain format
• ByteProcessor method / A sample plugin

C

• clustering
  • about / Clustering
• color images
  • about / Color and multichannel images
• Constrain aspect ratio option / Image resizing
• control structure
  • about / Control structures
  • for loop / The for loop
  • while loop / The while loop
  • if (condition) and if (condition) … else statements / The if (condition) and if (condition) … else statements

D

• 3D volume rendering
  • about / 3D volume rendering
• dialogCanceled variable / Adding a GUI to your plugin
• DICOM / Opening images with a certain format
• DICOM Rewriter
  • URL / Study anonymization
• digital images
  • about / Opening images with a certain format, 3D and 4D images – stacks and hyperstacks
• dimensions
  • of image, obtaining / Obtaining the dimensions of an image
• distance / Volume Viewer
• documentation
  • Windows, URL / Installing ImageJ
  • Mac OS, URL / Installing ImageJ
  • Linux, URL / Installing ImageJ
• DOES_8G, DOES_RGB, DOES_ALL constant / The PlugInFilter interface
• DOES_16, DOES_32, DOES_8C constant / The PlugInFilter interface
• DOES_ALL constant / Adding a GUI to your plugin
• DOES_STACKS constant / The PlugInFilter interface
• DONE constant / The PlugInFilter interface

E

• Eclipse IDE
  • ImageJ, setting up / Setting up ImageJ under the Eclipse IDE
• Eclipse ImageJ plugin
  • about / Our first Eclipse ImageJ plugin
• edge detection
  • about / Edge detection
• external libraries
  • using / Using external libraries

F

• FFT
  • about / The Fourier transform
• FigureJ
  • URL / FigureJ
• FIJI
  • about / FIJI (Fiji Is Not ImageJ)
  • URL / FIJI (Fiji Is Not ImageJ)
• File.openDialog(message) function / Opening an image from a macro
• FITS / Opening images with a certain format
• FloatProcessor object / A sample plugin
• for loop / The for loop
• Fourier transform
  • about / The Fourier transform
• frequency domain
  • image filtering / Image filtering in the frequency domain
• functions
  • about / Defining functions

G

• Gap between images / Reading raw data
• GenericDialog class / Adding a GUI to your plugin
• getNextNumber() method / Adding a GUI to your plugin
• GIF / Opening images with a certain format, Color and multichannel images
• Google Scholar
  • URL / What ImageJ is for (and what it is not for)
• GUI
  • adding, to plugins / Adding a GUI to your plugin
  • adding, to plugin / Adding a GUI to your plugin

H

• histogram
  • about / Image histogram and window/level parameters
• Hue, Saturation, Brightness (HSB) / Color and multichannel images

I

• IEEE Xplore
  • URL / What ImageJ is for (and what it is not for)
• if (condition) and if (condition) … else statements / The if (condition) and if (condition) … else statements
• image
  • regions, selecting for / Selecting regions of your image
  • opening, from macro / Opening an image from a macro
  • opened images, finding / Finding out how many images are open
  • dimensions, obtaining / Obtaining the dimensions of an image
  • specific image, selecting / Selecting a specific image
  • registration / Image registration
• image filtering
  • in spatial domain / Image filtering in the spatial domain
  • in frequency domain / Image filtering in the frequency domain
• ImageJ
  • about / ImageJ – history and motivation
  • installing / Installing ImageJ
  • stable version, URL for downloading / Installing ImageJ
  • window / First run
  • installation, updating / Updating the installation
  • configuration, options / Configuration options
  • memory limit, increasing / Memory limit increase
  • macro / What is an ImageJ macro
  • plugins / ImageJ plugins
  • setting up, under Eclipse IDE / Setting up ImageJ under the Eclipse IDE
• ImageJ Information and Documentation Portal
  • URL / Summary
• ImageJ plugin API
  • about / The ImageJ plugin API
• image overlay
  • about / The ROI manager and the image overlay
• ImagePlus object / A sample plugin
• ImageProcessor object / A sample plugin, The PlugInFilter interface
• images
  • opening, with certain format / Opening images with a certain format
  • title / Opening images with a certain format
  • properties, information text / Opening images with a certain format
  • digital image / Opening images with a certain format
  • online sample images / Online sample images
  • saving / Saving images
  • zomming in / Zooming on the image and pixel values
  • resizing / Image resizing
• image segmentation
  • about / Image segmentation
• installation
  • ImageJ / Installing ImageJ
  • ImageJ, on Windows / Windows
  • ImageJ, on Linux / Linux / Mac OS
  • ImageJ, on Mac OS / Linux / Mac OS
  • updating / Updating the installation

J

• Java
  • URL / Installing ImageJ
• jClustering
  • URL / Clustering
• JPG / Opening images with a certain format

L

• Laboratory for Optical and Computational Instrumentation (LOCI) / LOCI Bio-Formats
• lines
  • about / Basic selections – lines, length, and profiles
• Linux
  • ImageJ, installing / Linux / Mac OS
• Live button / Basic selections – lines, length, and profiles
• local thresholding / Auto Threshold and Auto Local Threshold
• LOCI Bio-Formats
  • about / LOCI Bio-Formats
• lookup table (LUT) / Opening images with a certain format

M

• Mac OS
  • ImageJ, installing / Linux / Mac OS
• macro
  • about / What is an ImageJ macro
  • reader / The macro recorder
  • running / Running macros
  • recorded macro, modifying / Modifying a recorded macro
  • language / More about the macro language – basic syntax and operators
  • debugging / A brief note on debugging a macro
  • on ImageJ website / Some useful procedures
  • image, opening from / Opening an image from a macro
  • speeding up / Speeding up a macro
  • GUI, adding to / Adding a GUI to your macro
  • installing / Installing macros for easy access
  • directory / Shared macros – the ImageJ macro directory
• Magnetic Resonance Imaging (MRI) / 3D and 4D images – stacks and hyperstacks
• Measure button / The ROI manager and the image overlay
• memory
  • limit, increasing / Memory limit increase
• MosaicJ
  • URL / MosaicJ

N

• NIH Image / ImageJ – history and motivation
• NO_UNDO constant / The PlugInFilter interface

O

• Offset to first image / Reading raw data

P

• particle analysis
  • about / Particle analysis
• PGM / Opening images with a certain format
• pixel / Opening images with a certain format
• pixel values
  • zooming in / Zooming on the image and pixel values
• PlugIn / A sample plugin
• PlugInFilter interface
  • about / A sample plugin, The PlugInFilter interface
• plugins
  • about / ImageJ plugins
  • installing / Installing a plugin
  • sample / A sample plugin
  • GUI, adding / Adding a GUI to your plugin
  • ImageJ plugin API / The ImageJ plugin API
  • Eclipse ImageJ plugin / Our first Eclipse ImageJ plugin
  • sharing / Sharing your plugin
• PNG / Opening images with a certain format
• profiles
  • about / Basic selections – lines, length, and profiles
• Projection Method / 3D and 4D images – stacks and hyperstacks
• pseudo color / Color and multichannel images
• PubMed
  • URL / What ImageJ is for (and what it is not for)

R

• RankFilters class / Adding a GUI to your plugin
• raw data
  • reading / Reading raw data
• regions
  • selecting, for image / Selecting regions of your image
• regions of interest
  • drawing, over area / Drawing regions of interest over an area
  • manager / The ROI manager and the image overlay
• requires(version) function / Adding a GUI to your macro
• results / Basic selections – lines, length, and profiles
• RGB / Color and multichannel images
• ROI_REQUIRED constant / The PlugInFilter interface
• run method / A sample plugin, The PlugInFilter interface

S

• Scale parameter / Volume Viewer
• segmentation
  • about / Thresholding
• selectImage(id) function / Selecting a specific image
• setBatchMode(arg) function / Speeding up a macro, The batch mode
• ShortProcessor method / A sample plugin
• SIOX
  • URL / SIOX (Simple Interactive Object Extraction)
• spatial domain
  • image filtering / Image filtering in the spatial domain
• Stack functions / A note on slices, frames, and channels
• Stackreg
  • about / Stackreg
• stacks / 3D and 4D images – stacks and hyperstacks
• STACK_REQUIRED constant / The PlugInFilter interface

T

• thresholding / Thresholding
• TIFF / Opening images with a certain format
• trainable Weka segmentation
  • URL / The trainable Weka segmentation
• Transfer Function / Volume Viewer

V

• variables
  • about / Variables
• var keyword / Installing macros for easy access
• Volume Viewer
  • about / Volume Viewer
• voxel / 3D and 4D images – stacks and hyperstacks

W

• while loop / The while loop
• Windows
  • ImageJ, installing / Windows