Index

A

• ActionBar
  • about / Installing macros
  • documentation, URL / Installing macros
• Add Macro Code selector / Running macros in batch process mode
• Apache Maven website
  • URL / Other resources
• Apache POI
  • URL / Other resources
• Application Programming Interface (API)
  • about / The Application Programming Interface
  • URL / The Application Programming Interface
• area selections
  • about / Area selections
  • rectangles / Area selections
  • oval / Area selections
• AstroImageJ
  • URL / ImageJ distributions

B

• basic measurements
  • about / Basic measurements
  • area selections, using / Area selections and measurements
  • line selections, using / Line selections and measurements
• basic measurements, with area selections
  • about / Area selections and measurements
  • rectangular selections / Area selections and measurements
  • oval selections / Oval selections
  • polygon selections / Polygon selections
• basic measurements, with line selections
  • about / Line selections and measurements
  • kymographs / Kymographs
  • line profiles, creating / Line profiles
• batch process mode
  • macros, running in / Running macros in batch process mode
• BeanShell / Macros and scripting languages
• Beanshell script / Installing macros
• BeanShell scripting
  • about / BeanShell scripting
  • ImageJ main class / ImageJ main class
  • image processing, functions / Functions to process images
  • selections, functions for / Functions for selections
  • saving / Saving and running your scripts
  • running / Saving and running your scripts
• Bio-formats
  • about / Bio-formats
• Bio-Formats plugin / ImageJ distributions, Images in ImageJ
• bleach correction
  • about / Bleach correction

C

• Coloc2 plugin / Coloc2
• colocalization
  • about / Colocalization
  • semiquantitative colocalization / Semiquantitative colocalization
• color images / Color images
  • thresholding / Thresholding color images
• ColorTransformer2 plugin / ColorTransformer2
• Command-line Interface (CLI) / Compiling SciJava plugins

D

• dark noise
  • correcting / Correcting dark noise
• Differential Interference Contrast (DIC) optic / Uneven illumination – background subtraction

E

• EM-CCD (Electron-Multiplying CCD) / Correcting dark noise
• external libraries
  • adding / Adding external libraries
  • dependency, adding for Apache POI / Adding the dependency for Apache POI
  • Excel file, creating / Creating an Excel file

F

• feature extraction
  • about / Feature extraction
  • edge detection / Edge detection
• FFMPEG plugin / The uses of ImageJ
• Fiji
  • URL / ImageJ distributions, Basic development
• File.directory() function / Saving an image to a folder
• frame / Time series

G

• gel quantification analysis
  • URL / Line profiles
• Git Book
  • URL / Additional tools
• Goutte_pendante plugin / Goutte_pendante
• grayscale images / Grayscale images
  • thresholding / Thresholding grayscale images

H

• HSB images / Color images
• HSSF moniker (Horrible SpreadSheet Format) / Adding the dependency for Apache POI
• hyperstacks
  • about / Stacks and hyperstacks

I

• Icy
  • URL / ImageJ distributions
• image, filtering
  • about / Image filtering
  • in frequency domain / Filtering in the frequency domain
  • in spatial domain / Image filtering in the spatial domain
• ImageJ
  • distributions / ImageJ distributions
  • basic package, URL / ImageJ distributions
  • uses / The uses of ImageJ
  • current state / The current state of ImageJ
  • integrated environment / Integrated environment for acquisition and processing
  • installation / Installation of ImageJ
  • Windows, installing on / Installing on Windows
  • Mac OS X, installing on / Installing on Mac OS X
  • Linux, installing on / Installing on Linux
  • folder structure / The ImageJ folder structure
  • fresh ImageJ installation / Configuring a fresh ImageJ installation
  • images / Images in ImageJ
  • selections / Selections and regions in ImageJ
  • regions / Selections and regions in ImageJ
  • area selections / Area selections
  • ellipses / Oval selections
  • ovals / Oval selections
  • source code, URL / Gathering all components
  • basic development / Basic development
  • tasks, URL / Basic development
  • online resource, URL / Basic development
  • tools / Additional tools
  • project management and feedback / Project management and feedback
  • resources / Other resources
• ImageJ, folder structure
  • plugins folder / Plugins folder
  • macros folder / Macros folder
• ImageJ2
  • about / ImageJ2
• ImageJ2 plugin
  • creating / Creating an ImageJ2 plugin
• ImageJ2 plugins / Frameworks for macros and plugins
• ImageJ Javadoc / ImageJ Javadoc
• ImagePlus class / ImagePlus
• ImageProcessor class / ImageProcessor
• images
  • about / Images in ImageJ
  • URL / Images in ImageJ
  • types / Image types
  • grayscale images / Grayscale images
  • color images / Color images, Color images and multichannel stacks
  • and pixel information, extracting / Extracting image and pixel information
  • loading / Loading images and sequences
  • saving / Saving images
  • calibrating / Image calibration
  • viewing, in ImageJ / Viewing images in ImageJ
  • multichannel images, viewing / Viewing multichannel images
  • time series, viewing / Viewing time series
  • correcting / Correcting images
  • technical background / Technical background
  • Shot noise, correcting / Correcting Shot noise
  • dark noise, correcting / Correcting dark noise
  • image normalization / Image normalization
  • bleach correction / Bleach correction
• image segmentation
  • about / Image segmentation
  • image thresholding / Image thresholding
  • grayscale images, thresholding / Thresholding grayscale images
• image thresholding
  • about / Image thresholding
  • grayscale images, thresholding / Thresholding grayscale images
  • URL / Thresholding grayscale images
  • color images, thresholding / Thresholding color images
• ImgLib2
  • URL / Basic development
• installation
  • macros / Installing macros

J

• JavaScript / Macros and scripting languages
• Java Virtual Machine (JVM) / Running and debugging plugins

K

• kernel / Image filtering in the spatial domain
• kymograph
  • creating / Line selections
  • about / Kymographs

L

• LAMP (Linux, Apache, MySQL, PHP) server distribution / Project management and feedback
• legacy plugins
  • about / Legacy plugins
  • PlugIn type / The PlugIn type
  • PlugInFilter type / The PlugInFilter type
  • PlugInFrame type / The PlugInFrame type
  • implementing / Implementing a legacy plugin
  • and macros, combining / Combining macros and legacy plugins
• line profiles
  • creating / Line profiles
• line selections
  • about / Line selections
• lookup table (LUT) / Grayscale images

M

• macro recorder / Recording macros
• macros
  • recording / Recording macros
  • recording, for conversion / Recording a macro for conversion
  • modifying / Modifying macros
  • user input / User input in macros
  • built-in functions, URL / User input in macros
  • progress, showing / Showing progress in macros
  • running, in batch process mode / Running macros in batch process mode
  • installing / Installing macros
  • framework / Frameworks for macros and plugins
  • and scripting languages / Macros and scripting languages
• macros progress
  • showing / Showing progress in macros
  • time series, processing / Processing the time series
• Magnetic Resonance Imaging (MRI) imaging / Processing Z-stacks
• Maven plugin project / Creating a Maven plugin project
• morphological operators
  • erode / Erode and dilate
  • dilate / Erode and dilate
  • skeletonize / Skeletonize and watershed
  • watershed / Skeletonize and watershed
• morphological processing
  • about / Morphological processing
  • morphological operators / Morphological operators
• MtrackJ plugin / MtrackJ
• multichannel images
  • viewing / Viewing multichannel images
• multichannel stacks
  • about / Color images and multichannel stacks
• multidimensional images
  • about / Multidimensional images
• Multi Kymograph tool / Kymographs
• MultipleKymograph plugin / MultipleKymograph
• My awesome tools (Mat) / Installing macros

N

• Netbeans
  • URL / Additional tools
• NetBeans IDE
  • setting up / Setting up NetBeans IDE
  • URL / Setting up NetBeans IDE
  • components, gathering / Gathering all components
  • project, setting up / Setting up a project
  • project, URL / Setting up a project
  • ImageJ, building / Building ImageJ
  • plugin, creating / Creating a plugin
  • documentation, creating / Creating documentation
  • ImageJ Javadoc / ImageJ Javadoc
  • Plugin Javadoc / Plugin Javadoc
  • Maven, used for developing plugins / Developing plugins using Maven
  • POM, constructing / Construction of the POM
  • Maven plugin project, creating / Creating a Maven plugin project
  • ImageJ2 plugin, creating / Creating an ImageJ2 plugin
  • pros / Pros and cons of using an IDE
  • cons / Pros and cons of using an IDE
• NIH
  • URL / Installing on Windows

O

• OME-XML (Open Microscopy Environment-XML) project
  • about / SciFIO and OME-XML
• Open… button / Running macros in batch process mode

P

• particle analysis
  • semiquantitative colocalization / Particle analysis
  • preprocessing / Preprocessing and preparations
  • preparations / Preprocessing and preparations
• plugin
  • background / Plugin background and goal
  • goal / Plugin background and goal
  • project setup / Basic project setup
  • user interaction, adding / Adding user interaction and preferences
  • preferences, adding / Adding user interaction and preferences
  • options dialog / Settings and options dialog
  • settings dialog / Settings and options dialog
  • sharing / Sharing your plugin
  • site, creating / Creating a site
  • Wiki login page, URL / Creating a site
  • uploading / Uploading your plugin
• PlugInFilter
  • creating / Creating a basic PlugInFilter
  • current implementation, testing / Testing our current implementation
  • setup method, implementing / Implementing the setup method
  • measurements, implementing / Implementing the measurements
• PlugInFilter type / The PlugInFilter type
• PlugInFrame type / The PlugInFrame type
• Plugin Javadoc / Plugin Javadoc
• plugins
  • framework / Frameworks for macros and plugins
  • about / Plugins for ImageJ
  • ImageJ main class / ImageJ main class
  • WindowManager class / WindowManager
  • ImagePlus class / ImagePlus
  • ImageProcessor class / ImageProcessor
  • RoiManager class / RoiManager
  • Roi class / The Roi class
  • anatomy / The basic anatomy of a plugin
  • legacy plugins / Legacy plugins
  • running / Running and debugging plugins
  • debugging / Running and debugging plugins, Debugging plugins
  • compiling / Compiling plugins
  • SciJava plugins, compiling / Compiling SciJava plugins
  • examples / Examples of available plugins
  • in ImageJ / Example plugins available in ImageJ and Fiji
  • in Fiji / Example plugins available in ImageJ and Fiji
  • MultipleKymograph / MultipleKymograph
  • ColorTransformer2 / ColorTransformer2
  • MtrackJ / MtrackJ
  • Coloc2 / Coloc2
  • Goutte_pendante / Goutte_pendante
• PlugIn type / The PlugIn type
• Point ROI / Selections and regions in ImageJ
• point selections
  • about / Point selections
• Poisson process / Correcting Shot noise
• POM file / Construction of the POM

R

• regions
  • about / Selections and regions in ImageJ
  • area selections / Selections and regions in ImageJ
  • line selections / Selections and regions in ImageJ
• Regions Of Interest (ROIs) / Selections and regions in ImageJ
• Roi class / The Roi class
• ROI Manager / Selections and regions in ImageJ
• RoiManager class / RoiManager
• run() method / Modifying macros
• run method, PlugInFilter
  • implementing / Implementing the run method
  • object, detecting / Detecting an object
  • detection, refining / Refining the detection
  • multiple objects, detecting / Detecting multiple objects
• Runtime Environment (JRE) / Obtaining and installing ImageJ

S

• saveAs command / Saving an image to a folder
• SciFIO
  • about / SciFIO and OME-XML
• Scijava plugins
  • about / SciJava plugins
  • @Plugin annotation / The @Plugin annotation
  • services / Services
  • commands / Commands
  • compiling / Compiling SciJava plugins
• segmentation / Image segmentation
• selections
  • area selections / Area selections
  • line selections / Line selections
  • point selections / Point selections
• sequences
  • loading / Loading images and sequences
• setup method, PlugInFilter
  • return type / The return type and autocomplete
  • auto-complete / The return type and autocomplete
  • Javadoc, for methods / Javadoc for methods
  • finishing / Finishing the setup method
• Shot noise
  • correcting / Correcting Shot noise
• signal-to-noise ratio (SNR) / Correcting Shot noise
• signal processing
  • URL / Basic development
• stack
  • about / Stacks and hyperstacks
• stack processing
  • about / Stack processing
  • Z stacks, processing / Processing Z-stacks
  • projections / Stack projections
  • maximum projection / Maximum projection
  • volume, viewing / Volume viewing and rendering
  • volume, rendering / Volume viewing and rendering
  • time series, processing / Processing time series
  • time series data, normalizing / Normalizing time series data
  • time series data, processing / Normalizing time series data
• Subversion
  • URL / Additional tools
• syntax highlighting / Recording a macro for conversion

T

• Tagged Image File Format (TIFF) / The uses of ImageJ
• time series
  • about / Time series
  • viewing / Viewing time series
  • uneven illumination / Uneven illumination – background subtraction
  • processing / Processing time series
  • data, normalizing / Normalizing time series data
• tools
  • about / Additional tools

U

• user input, macro
  • about / User input in macros
  • specific file, opening / Opening a specific file
  • image, saving to folder / Saving an image to a folder
  • choices, adding / Adding choices
  • input check, performing / Performing input checking

V

• volumes
  • about / Z-stack images and volumes
• Volume Viewer / Volume viewing and rendering

W

• WindowManager class / WindowManager

Z

• Z-stack
  • about / Stacks and hyperstacks
• Z stack images
  • about / Z-stack images and volumes
• Z stacks
  • processing / Processing Z-stacks