Getting started This part provides basic information on ImageJ installation, troubleshooting and update strategies It discusses Fiji and ImageJ2 as well as third-party software related to ImageJ. Being impossible to document all the capabilities of Image J without exploring technical aspects of image processing, external resources allowing willing readers to know more about digital signal processing are also Introduction ImageJ is a public domain Java image processing and analysis program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.5 or later virtual machine. Downloadable distributions are available for Windows, Mac OSX and Linux. It can display, edit, analyze, process, save and print 8-bit 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and raw. It supports'stacks'(and hyperstacks), a series of images that share a ingle window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations It can calculate area and pixel value statistics of user-defined selections. It can measure distances d angles. It can create density histograms and line profile plots. It supports standard image processing functions such as contrast manipulation, sharpening, smoothing, edge detection and median filtering It does geometric transformations such as scaling, rotation and fips. Image can be zoomed up te 32: 1 and down to 1: 32. All analysis and processing functions are available at any magnification factor. The program supports any number of windows(images) simultaneously, limited only by available memory Spatial calibration is available to provide real world dimensional measurements in units such as millimeters. Density or gray scale calibration is also available ImageJ was designed with an open architecture that provides extensibility via Java plugins Custom acquisition, analysis and processing plugins can be developed using ImageJ's built in editor and Java compiler. User-written plugins make it possible to solve almost any image processing or analysis problem Being public domain open source software, an ImageJ user has the four essential freedoms defined by the Richard Stallman in 1986: 1)The freedom to run the program, for any purpose; 2 )The freedom to study how the program works, and change it to make it do what you wish; 3) The freedom to redistribute copies so you can help your neighbor; 4)The freedom to improve the program, and release your improvements to the public, so that the whole community benefits Image is being developed on Mac OSX using its built in editor and Java compiler, plus the BBEdit editor and the Ant build tool. The source code is freely available. The author, Wayne Rasband(wsr @nih. gov), is a Special Volunteer at the National Institute of Mental Health ethesda, Maryland, USA SEE ALSO: History of ImageJ at imagejdev, org AsomehowoutdatedlistofImagej'sfeaturesisavailableathttp://imagej.nihgov/ij/features.html
Part I Getting Started This part provides basic information on ImageJ installation, troubleshooting and update strategies. It discusses Fiji and ImageJ2 as well as third-party software related to ImageJ. Being impossible to document all the capabilities of ImageJ without exploring technical aspects of image processing, external resources allowing willing readers to know more about digital signal processing are also provided. 1 Introduction ImageJ is a public domain Java image processing and analysis program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.5 or later virtual machine. Downloadable distributions are available for Windows, Mac OS X and Linux. It can display, edit, analyze, process, save and print 8–bit, 16–bit and 32–bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and ‘raw’. It supports ‘stacks’ (and hyperstacks), a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations1 . It can calculate area and pixel value statistics of user-defined selections. It can measure distances and angles. It can create density histograms and line profile plots. It supports standard image processing functions such as contrast manipulation, sharpening, smoothing, edge detection and median filtering. It does geometric transformations such as scaling, rotation and flips. Image can be zoomed up to 32 : 1 and down to 1 : 32. All analysis and processing functions are available at any magnification factor. The program supports any number of windows (images) simultaneously, limited only by available memory. Spatial calibration is available to provide real world dimensional measurements in units such as millimeters. Density or gray scale calibration is also available. ImageJ was designed with an open architecture that provides extensibility via Java plugins. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built in editor and Java compiler. User-written plugins make it possible to solve almost any image processing or analysis problem. Being public domain open source software, an ImageJ user has the four essential freedoms defined by the Richard Stallman in 1986: 1) The freedom to run the program, for any purpose; 2) The freedom to study how the program works, and change it to make it do what you wish; 3) The freedom to redistribute copies so you can help your neighbor; 4) The freedom to improve the program, and release your improvements to the public, so that the whole community benefits. ImageJ is being developed on Mac OS X using its built in editor and Java compiler, plus the BBEdit editor and the Ant build tool. The source code is freely available. The author, Wayne Rasband (wsr@nih.gov), is a Special Volunteer at the National Institute of Mental Health, Bethesda, Maryland, USA. See also: History of ImageJ at imagejdev.org 1A somehow outdated list of ImageJ’s features is available at http://imagej.nih.gov/ij/features.html 1
Installing and Maintaining ImageJ 2 Installing and Maintaining ImageJ Imagejcanbedownloadedfromhttp://imagej.nihgov/ij/download.htmlDetailsonhow toinstallImagejonLinux,MacOs9,MacOsXandWindows[1]areavailableathttp /imagej. nih. gov /ij/docs/install/(Help b Installation.. command). Specially useful are the platform-specific Troubleshooting and Known Problems sections. Fiji installation is described at http://fiji.sc/wiki/index.php/downloads The downloaded package may not contain the latest bug fixes so it is recommended to upgrade ImageJ right after a first installation. Updating IJ consists only of running Help b Update ImageJ .. which will install the latest Bij jar in the ImageJ folder(on Linux and Windows) or inside the Image J app(on Mac OsX) Help D Update ImageJ.. can be used to upgrade(or downgrade) the Eij. jar file to release updates or daily builds. Release updates are announced frequently on the IJ news website and are labelled alphabetically(e.g, v 1. 43m). Typically, these releases contain several new features and bug fixes, described in detail on the ImageJ News page. Daily builds, on the other hand, are labelled with numeric sub-indexes(e. g, v. 1.43n4)and are often released without documentation. Nevertheless, if available, release notes for daily builds can be found at http://imagej.nihgov/ij/source/release-notes.htmlWhenareleasecycleends(v.1.42ended with 1.42q, v 1.43 with 1.43u, etc. )an installation package is created, downloadable from http://imagej.nih.gov/ij/download.htmlTypically,thispackageisbundledwithasmalllistof add-ons(Macros, Scripts and Plugins) SEE ALSO: Luts, Macros and Tools Updater, a macro toolset that performs live-updating of macros listed on the Image web site 2.1 mage Distributions Image alone is not that powerful: it's real strength is the vast repertoire of Plugins that extend ImageJ's functionality beyond its basic core. The many hundreds, probably thousands, freely available plugins from contributors around the world play a pivotal role in ImageJ's success 22] Running Help b Update ImageJ ., however, will not update any of the plugins you may have stalled ImageJ add-ons(Plugins, Scripts and Macros)are available from several sources(ImageJ's plugins page [ HelpD Plugins.., ImageJ Information and Documentation Portal and Fiji's webpage, among others) making manual updates of a daunting task. This reason alone, makes it extremely convenient the use of Image Distributions bundled with a pre-organized collection of dd-ons Below is a list of the most relevant projects that address the seeming difficult task of organizing and maintaining ImageJ beyond its basics. If you are a life scientist and have doubts about which distribution to choose you should opt for Fiji. It is heavily maintained, offers an automatic updater, improved scripting capabilities and ships with powerful plugins. More specialized adaptations of ImageJ are discussed in Software Packages Built on Top of ImageJ Fiji(Fiji Is Just ImageJ-Batteries included) is a distribution of Image J together with Java, Java 3D and several plugins organized into a coherent menu structure. Citing its developers Certain plugins, however, provide self-updating mechanisms (e. g, Object J and the OME Bio-Formats Last updated: 2012/10/02
Installing and Maintaining ImageJ 2 Installing and Maintaining ImageJ ImageJ can be downloaded from http://imagej.nih.gov/ij/download.html. Details on how to install ImageJ on Linux, Mac OS 9, Mac OS X and Windows [1] are available at http: //imagej.nih.gov/ij/docs/install/ (Help . Installation. . . command). Specially useful are the platform-specific Troubleshooting and Known Problems sections. Fiji installation is described at http://fiji.sc/wiki/index.php/Downloads. The downloaded package may not contain the latest bug fixes so it is recommended to upgrade ImageJ right after a first installation. Updating IJ consists only of running Help .Update ImageJ. . . , which will install the latest ij.jar in the ImageJ folder (on Linux and Windows) or inside the ImageJ.app (on Mac OS X). Help .Update ImageJ. . . can be used to upgrade (or downgrade) the ij.jar file to release updates or daily builds. Release updates are announced frequently on the IJ news website and are labelled alphabetically (e.g., v. 1.43m). Typically, these releases contain several new features and bug fixes, described in detail on the ImageJ News page. Daily builds, on the other hand, are labelled with numeric sub-indexes (e.g., v. 1.43n4) and are often released without documentation. Nevertheless, if available, release notes for daily builds can be found at http://imagej.nih.gov/ij/source/release-notes.html. When a release cycle ends (v. 1.42 ended with 1.42q, v. 1.43 with 1.43u, etc.) an installation package is created, downloadable from http://imagej.nih.gov/ij/download.html. Typically, this package is bundled with a small list of add-ons (Macros, Scripts and Plugins). See also: Luts, Macros and Tools Updater, a macro toolset that performs live-updating of macros listed on the ImageJ web site 2.1 ImageJDistributions ImageJ alone is not that powerful: it’s real strength is the vast repertoire of Plugins that extend ImageJ’s functionality beyond its basic core. The many hundreds, probably thousands, freely available plugins from contributors around the world play a pivotal role in ImageJ’s success [22]. Running Help .Update ImageJ. . . , however, will not update any of the plugins you may have installed1 . ImageJ add-ons (Plugins, Scripts and Macros) are available from several sources (ImageJ’s plugins page [Help . Plugins. . . ], ImageJ Information and Documentation Portal and Fiji’s webpage, among others) making manual updates of a daunting task. This reason alone, makes it extremely convenient the use of ImageJDistributions bundled with a pre-organized collection of add-ons. Below is a list of the most relevant projects that address the seeming difficult task of organizing and maintaining ImageJ beyond its basics. If you are a life scientist and have doubts about which distribution to choose you should opt for Fiji. It is heavily maintained, offers an automatic updater, improved scripting capabilities and ships with powerful plugins. More specialized adaptations of ImageJ are discussed in Software Packages Built on Top of ImageJ. Fiji Fiji (Fiji Is Just ImageJ—Batteries included) is a distribution of ImageJ together with Java, Java 3D and several plugins organized into a coherent menu structure. Citing its developers, 1Certain plugins, however, provide self-updating mechanisms (e.g., ObjectJ and the OME Bio-Formats). 2 Last updated: 2012/10/02
Installing and Maintaining ImageJ Related software Fiji compares to ImageJ as Ubuntu compares to Linux". The main focus of Fiji is to assist search in life sciences, targeting image registration, stitching, segmentation, feature extraction and 3D visualization, among others. It also supports many scripting languages(Bean Script Clojure, Jython, Python, Ruby, see Scripting in Other Languages). Importantly, Fiji ships with a convenient updater that knows whether your files are up-to-date, obsolete or locally modified Comprehensive documentation is available for most of its plugins. The Fiji project was presented publicly for the first time at the ImageJ User and Developer Conference in November 2008 MBF ImageJ The MBF ImageJ bundle or Image/ for Microscopy(formerly WCIF-ImageJ) features a collection f plugins and macros, collated and organized by Tony Collins at the MacBiophotonics facility, McMaster University. It is accompanied by a comprehensive manual describing how to use the bundle with light microscopy image data. It is a great resource for microscopists but is not maintained actively, lagging behind the development of core ImageJ Note that you can add plugins from MBF Image J to Fiji, combining the best of both programs Actually, you can use multiple Image J distributions simultaneously, assemble your own ImageJ bundle by gathering the plugins that best serve your needs (probably, someone else at your itution already started one? or create symbolic links to share plugins between different allations SEE ALSO: Description of all Image J related projects at Image Dev 2.2 Related Software 2.2.1 Software Packages Built on Top of ImageJ Bio7 Bio7 is an integrated development environment for ecological modeling with a main focus on individual based modeling and spatially explicit models. Bio7 features: Statistical analysis(using R); Spatial statistics; Fast communication between R and Java; Bean Shell and Groovy support; Sensitivity analysis with an embedded flowchart editor and creation of 3D OpenGL (Jogl) models(see also RImageJ in ImageJ Interoperability) BoneJ BoneJ is a collection of tools for trabecular geometry and whole bone shape analysis pManager Micro-Manager is a software package for control of automated microscopes. It lets you execute common microscope image acquisition strategies such as time-lapses, multi channel imaging, z-stacks, and combinations thereof. IManager works with microscopes from all four major manufacturers, most scientific-grade cameras and many peripherals used in microscope imaging MRI-CIA MRI Cell Image Analyzer, developed by the Montpellier RIO Imaging facility (CNRS), is a rapid image analysis application development framework, adding visual scripting interface to ImageJ's capabilities. It can create batch applications as well as interactive applications. The applications include the topics"DNA combing", " quantification of stained proteins in cells", " comparison of intensity ratios between nuclei and cytoplasm and "counting nuclei stained in different channels Object ObjectJ, the successor of object-image, supports graphical vector objects that non- destructively mark images on a transparent layer. Vector objects can be placed manually or by macro commands. Composite objects can encapsulate different color-coded marker Last updated: 2012/10/02
Installing and Maintaining ImageJ Related Software “Fiji compares to ImageJ as Ubuntu compares to Linux”. The main focus of Fiji is to assist research in life sciences, targeting image registration, stitching, segmentation, feature extraction and 3D visualization, among others. It also supports many scripting languages (BeanScript, Clojure, Jython, Python, Ruby, see Scripting in Other Languages). Importantly, Fiji ships with a convenient updater that knows whether your files are up-to-date, obsolete or locally modified. Comprehensive documentation is available for most of its plugins. The Fiji project was presented publicly for the first time at the ImageJ User and Developer Conference in November 2008. MBF ImageJ The MBF ImageJ bundle or ImageJ for Microscopy (formerly WCIF-ImageJ) features a collection of plugins and macros, collated and organized by Tony Collins at the MacBiophotonics facility, McMaster University. It is accompanied by a comprehensive manual describing how to use the bundle with light microscopy image data. It is a great resource for microscopists but is not maintained actively, lagging behind the development of core ImageJ. Note that you can add plugins from MBF ImageJ to Fiji, combining the best of both programs. Actually, you can use multiple ImageJ distributions simultaneously, assemble your own ImageJ bundle by gathering the plugins that best serve your needs (probably, someone else at your institution already started one?) or create symbolic links to share plugins between different installations. See also: Description of all ImageJ related projects at ImageDev 2.2 Related Software 2.2.1 Software Packages Built on Top of ImageJ Bio7 Bio7 is an integrated development environment for ecological modeling with a main focus on individual based modeling and spatially explicit models. Bio7 features: Statistical analysis (using R); Spatial statistics; Fast communication between R and Java; BeanShell and Groovy support; Sensitivity analysis with an embedded flowchart editor and creation of 3D OpenGL (Jogl) models (see also RImageJ in ImageJ Interoperability). BoneJ BoneJ is a collection of tools for trabecular geometry and whole bone shape analysis. µManager Micro-Manager is a software package for control of automated microscopes. It lets you execute common microscope image acquisition strategies such as time-lapses, multichannel imaging, z-stacks, and combinations thereof. µManager works with microscopes from all four major manufacturers, most scientific-grade cameras and many peripherals used in microscope imaging. MRI–CIA MRI Cell Image Analyzer, developed by the Montpellier RIO Imaging facility (CNRS), is a rapid image analysis application development framework, adding visual scripting interface to ImageJ’s capabilities. It can create batch applications as well as interactive applications. The applications include the topics “DNA combing”, “quantification of stained proteins in cells”, “comparison of intensity ratios between nuclei and cytoplasm” and “counting nuclei stained in different channels”. ObjectJ ObjectJ, the successor of object-image, supports graphical vector objects that nondestructively mark images on a transparent layer. Vector objects can be placed manually or by macro commands. Composite objects can encapsulate different color-coded marker 3 Last updated: 2012/10/02
aining ImageJ Related Software structures in order to bundle features that belong together. Object provides back-and- forth navigation between results and images. The results table supports statistics, sorting color coding, qualifying and macro access SalsaJ Salsa J is a student-friendly software developed specifically for the EU-HOU project It is dedicated to image handling and analysis of astronomical images in the classroom Salsa j has been translated into several languages TrakEM2 TrakEM2 is a program for morphological data mining, three-dimensional modeling and image stitching, registration, editing and annotation [13. TrakEM2 is distributed with Fiji and capable of 3D modeling Objects in 3D, defined by sequences of contours, or profiles, from which a skin, or mesh can be constructed and visualized in 3D Relational modeling The extraction of the map that describes links between objects. neuron contac ts which other neurons through how many and which synapses SEE ALSO: BiolmageXD, Endrov, Image SXM ImageJ Inter Several packages exist that allow ImageJ to interact with other applications/environments Bitplane Imaris ImarisXT can load and execute ImageJ plugins. bpImarisAdapter(W only and requiring valid licenses for Imaris and ImarisXT) allows the exchange of between Imaris and ImageJ CellProfiler CellProfiler [17 features RunImageJ, a module that allows ImageJ plugins to be run in a CellProfiler pipeline Icy Icy, an open source community software for bio-imaging, executes ImageJ plugins with almost 100% plugin compatibility Knime Knime(Konstanz Information Miner) contains several image processing nodes(KNIP) that are capable of executing Image plugins and macros Open Microscopy Environment All Open Microscopy Environment projects such as Bio- Formats, Vis Bio and OMERO integrate well with ImageJ RImageJ-R bindings for ImageJ Bindings between ImageJ and R (GNU S)-The free software environment for statistical computing and graphics. The documentation for RimaGejisavailableathttp://cran.r-project.org/web/packages/rimagej/rimagej.pdf (see also Bio7 in Software Packages Built on Top of Image J) MIJ- Matlab-ImageJ bi-directional communication A Java package for bi-directional data exchange between Matlab and ImageJ, allowing to exchange images between the two imaging software. MIJ also allows MATLAB to access all built-in functions of ImageJ as well as third-party ImageJ plugins. The developers provide more information on the MIJ and Matlab File Exchange websites. Fiji features Miji. m, which makes even more convenient to use the libraries and functions provided by Fijis components from within Matlab SEE ALSO: Image related links, list of related imaging software on the Image 2 website Last updated: 2012/10/02
Installing and Maintaining ImageJ Related Software structures in order to bundle features that belong together. ObjectJ provides back-andforth navigation between results and images. The results table supports statistics, sorting, color coding, qualifying and macro access. SalsaJ SalsaJ is a student-friendly software developed specifically for the EU-HOU project. It is dedicated to image handling and analysis of astronomical images in the classroom. SalsaJ has been translated into several languages. TrakEM2 TrakEM2 is a program for morphological data mining, three-dimensional modeling and image stitching, registration, editing and annotation [13]. TrakEM2 is distributed with Fiji and capable of: 3D modeling Objects in 3D, defined by sequences of contours, or profiles, from which a skin, or mesh, can be constructed, and visualized in 3D. Relational modeling The extraction of the map that describes links between objects. For example, which neuron contacts which other neurons through how many and which synapses. See also: BioImageXD, Endrov, Image SXM 2.2.2 ImageJ Interoperability Several packages exist that allow ImageJ to interact with other applications/environments: Bitplane Imaris ImarisXT can load and execute ImageJ plugins. bpImarisAdapter (Windows only and requiring valid licenses for Imaris and ImarisXT) allows the exchange of images between Imaris and ImageJ. CellProfiler CellProfiler [17] features RunImageJ, a module that allows ImageJ plugins to be run in a CellProfiler pipeline. Icy Icy, an open source community software for bio-imaging, executes ImageJ plugins with almost 100% plugin compatibility. Knime Knime (Konstanz Information Miner) contains several image processing nodes (KNIP) that are capable of executing ImageJ plugins and macros. Open Microscopy Environment All Open Microscopy Environment projects such as BioFormats, VisBio and OMERO integrate well with ImageJ. RImageJ — R bindings for ImageJ Bindings between ImageJ and R (GNU S) — The free software environment for statistical computing and graphics. The documentation for RImageJ is available at http://cran.r-project.org/web/packages/RImageJ/RImageJ.pdf (see also Bio7 in Software Packages Built on Top of ImageJ). MIJ — Matlab–ImageJ bi-directional communication A Java package for bi-directional data exchange between Matlab and ImageJ, allowing to exchange images between the two imaging software. MIJ also allows MATLAB to access all built-in functions of ImageJ as well as third-party ImageJ plugins. The developers provide more information on the MIJ and Matlab File Exchange websites. Fiji features Miji.m, which makes even more convenient to use the libraries and functions provided by Fiji’s components from within Matlab. See also: ImageJ related links, list of related imaging software on the ImageJ2 website 4 Last updated: 2012/10/02
2.3 ImageJ2 ImageJDev is a federally funded, multi-institution project dedicated to the development of the next-generation version of ImageJ: "ImageJ2". Image J2 is a complete rewrite of ImageJ that includes the current, stable version Image J(ImageJ1 ")with a compatibility layer so that old-style plugins and macros can run the same as they currently do in ImageJl. Below is a summary of the Image JDev project aims To create the next generation version of ImageJ and improve its core architecture based on the needs of the community To ensure ImageJ remains useful and relevant to the broadest possible community, main taining backwards compatibility with Image Jl as close to 100% as possible xpand functionality by interfacing Image J with existing open-source programs To lead ImageJ development with a clear vision, avoiding duplication of efforts To provide a central online resource for Image J: program downloads, a plugin repository, developer resources and more Be sure to follow the ImageJ2 project news and the Image Dev blog for updates on this excitin project 3 Getting Hely 3.1 Help on Image Analysis below is of online resources(in no particular order) related to image processing and clentlnc analysis, complementing the list of external resources on the IJ web site Ethics in Scientific Image Processing Online learning Tool for Research Integrity and Image Processing This website, created by the Office of Research Integrity, explains what is appropriate in image processing in science and what is not Digital Imaging: Ethics(at the Cellular Imaging Facily Core, SEHSC) This website, compiled by Douglas Cromey at the University of Alabama- Birmingham discusses thoroughly the topic of digital imaging ethics. It is recommended for all scientist The website contains links to several external resources including. 1. What's in a picture? The temptation of image manipulation(2004)M Rossner and K M Yamada, J Cell Biology 166(1): 11-15, doi: 10.1083 /jcb. 200406019 2. Not picture-perfect(2006), Nature 439, 891-892, doi: 10.1038/439891b Scientific Image Processing What you need to know about scientific image processing Simple and clear, this Fiji webpage explains basic aspects of scientific image processing Last updated: 2012/10/02
Getting Help ImageJ2 2.3 ImageJ2 ImageJDev is a federally funded, multi-institution project dedicated to the development of the next-generation version of ImageJ: “ImageJ2”. ImageJ2 is a complete rewrite of ImageJ, that includes the current, stable version ImageJ (“ImageJ1”) with a compatibility layer so that old-style plugins and macros can run the same as they currently do in ImageJ1. Below is a summary of the ImageJDev project aims: – To create the next generation version of ImageJ and improve its core architecture based on the needs of the community. – To ensure ImageJ remains useful and relevant to the broadest possible community, maintaining backwards compatibility with ImageJ1 as close to 100% as possible. – Expand functionality by interfacing ImageJ with existing open-source programs. – To lead ImageJ development with a clear vision, avoiding duplication of efforts – To provide a central online resource for ImageJ: program downloads, a plugin repository, developer resources and more. Be sure to follow the ImageJ2 project news and the ImageDev blog for updates on this exciting project. 3 Getting Help 3.1 Help on Image Analysis Below is a list of online resources (in no particular order) related to image processing and scientific image analysis, complementing the list of external resources on the IJ web site. Ethics in Scientific Image Processing – Online learning Tool for Research Integrity and Image Processing This website, created by the Office of Research Integrity, explains what is appropriate in image processing in science and what is not. – Digital Imaging: Ethics (at the Cellular Imaging Facily Core, SEHSC) This website, compiled by Douglas Cromey at the University of Alabama – Birmingham, discusses thoroughly the topic of digital imaging ethics. It is recommended for all scientists. The website contains links to several external resources, including: 1. What’s in a picture? The temptation of image manipulation (2004) M Rossner and K M Yamada, J Cell Biology 166(1):11–15, doi:10.1083/jcb.200406019 2. Not picture-perfect (2006), Nature 439, 891–892, doi:10.1038/439891b. Scientific Image Processing – What you need to know about scientific image processing Simple and clear, this Fiji webpage explains basic aspects of scientific image processing. 5 Last updated: 2012/10/02