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)
- 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
- 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
- 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