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1 change: 0 additions & 1 deletion _pages/404.md
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---
autogenerated: true
title: 404
description: test description
---

Oops! Were you looking for...
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1 change: 0 additions & 1 deletion _pages/Amccall.md
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---
autogenerated: true
title: Amccall
description: test description
---

The Amccall [ ImageJ update site](/update-sites) (sites.imagej.net/Amccall) installs the [Colocalization by Cross Correlation](/plugins/colocalization-by-cross-correlation) plugin.
1 change: 0 additions & 1 deletion _pages/Brightness_and_Contrast.md
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autogenerated: true
title: Brightness and Contrast
categories: Cookbook, tutorials
description: test description
---

**Note:** This page refers to the version of [ImageJ2](/software/imagej2) currently in development. For more information on using [Fiji](/fiji) and [ImageJ 1.x](/software/imagej1), please reference the [Fiji tutorials](Category_Tutorials) and [ImageJ 1.x documentation](/ij/docs/).
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1 change: 0 additions & 1 deletion _pages/Build_ImageJ2_Plugin_With_JavaFX.md
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autogenerated: true
title: Build ImageJ2 Plugin With JavaFX
categories: development
description: test description
---

**JavaFX** is the new graphical toolkit that will on the long term probably **replace Swing**. This page aims to give some guidelines to be able to build ImageJ2 plugin with JavaFX.
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1 change: 0 additions & 1 deletion _pages/Command_Line_Tips_and_Tricks.md
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autogenerated: true
title: Command Line Tips and Tricks
categories: tutorials
description: test description
---

This page lists all kinds of usable hints how to use the command line in the different environments supported by Fiji.
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1 change: 0 additions & 1 deletion _pages/Communication.md
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autogenerated: true
title: Communication
categories: Help
description: test description
---

There are several popular communication channels: {% include communication%}
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1 change: 0 additions & 1 deletion _pages/Diadem_Challenge_Data.md
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title: Diadem Challenge Data
categories: Tutorials
description: test description
---

This page describes how to visualize the various data sets provided as part of the [Diadem Challenge](http://www.diademchallenge.org/) in Fiji, and in particular viewing the traced neurons with [Simple Neurite Tracer](/plugins/snt). The most important point about this is that the SWC files distributed as part of the challenge all use co-ordinates that are image-coordinates rather than world co-ordinates. (This isn't how I interpret [the paper that describes the SWC format](http://dx.doi.org/10.1016/S0165-0270(98)00091-0), but in practice different software uses different conventions, so one has to deal with both.) This means that you should always select the "ignore image calibration" option when importing the SWC file into Simple Neurite Tracer. The other key point is that the image data are distributed with each slice in a separate TIFF file and don't specify the slice separation in those files. So, after importing the sequence you will need to correct the calibration according to information on the Diadem challenge website or they will look odd when rendered in 3D. I describe these steps in more detail below.
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1 change: 0 additions & 1 deletion _pages/FSTRPCParadigm.md
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---
autogenerated: true
title: FSTRPCParadigm
description: test description
---

It is implementation of RPCParadigm that executes commands in different instances of running Fiji. The Fiji can run in a different computer or a HPC cluster. Communication is realized through TCP/IP and data are serialized by library [fst](https://github.com/RuedigerMoeller/fast-serialization). It is possible to send as parameter in request every serializable object . Support for another types could be added through the offered extensibility. It is necessary to implement the interface *ParallelizationParadigmSerializer*:
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1 change: 0 additions & 1 deletion _pages/Find_Maxima....md
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---
autogenerated: true
title: Find Maxima...
description: test description
---

Determines the local maxima in an image and creates a binary (mask-like) image of the same size with the maxima, or one segmented particle per maximum, marked \[29\]. Analysis is performed on the existing rectangular selection or on the entire image if no selection is present. For RGB images, maxima of luminance are selected, with the luminance defined as weighted or unweighted average of the colors depending on how Weighted RGB to Grayscale Conversion is set in {% include bc path="Edit | Options | Conversions..." %}.
1 change: 0 additions & 1 deletion _pages/Finer_Grained_Debian_Packages.md
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autogenerated: true
title: Finer Grained Debian Packages
description: test description
---

{% include outdated %}
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1 change: 0 additions & 1 deletion _pages/First-instar_brain_6.3MB.md
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autogenerated: true
title: First-instar brain (6.3MB)
description: test description
---

The [Drosophila first-instar larval brain](https://fiji.sc/samples/first-instar-brain.zip) sample was provided by Albert Cardona to give a common test sample for segmentation of blob-like structures.
1 change: 0 additions & 1 deletion _pages/FunImageJ.md
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---
autogenerated: true
title: FunImageJ
description: test description
---


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1 change: 0 additions & 1 deletion _pages/Gauss_ImgLib2.md
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---
autogenerated: true
title: Gauss ImgLib2
description: test description
---

<figure><img src="/media/Gauss.png" title="Visualizes the offsets and sizes required to perform an n-dimensional gaussian convolution" width="750" alt="Visualizes the offsets and sizes required to perform an n-dimensional gaussian convolution" /><figcaption aria-hidden="true">Visualizes the offsets and sizes required to perform an n-dimensional gaussian convolution</figcaption></figure>
1 change: 0 additions & 1 deletion _pages/Gauss_Package_ImgLib2.md
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---
autogenerated: true
title: Gauss Package ImgLib2
description: test description
---

{% include info-box software='Fiji/ImgLib2' name='Gaussian Convolution' author='Stephan Preibisch' maintainer='Stephan Preibisch' source='https://fiji.sc/git/?p=imglib.git;a=tree;f=algorithms/core/src/main/java/net/imglib2/algorithm/gauss;hb=refs/heads/master' released='20 December 2011' latest-version='20 December 2011' status='active' website='http://fly.mpi-cbg.de/preibisch' %}
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1 change: 0 additions & 1 deletion _pages/Help_on_Menu_Item.md
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autogenerated: true
title: Help on Menu Item
categories: Help
description: test description
---

The convenient command {% include bc path='Help | Help on Menu Item'%} allows you to open pages on specific menu items:
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1 change: 0 additions & 1 deletion _pages/Hippocampal_CA3_Interneuron.md
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autogenerated: true
title: Hippocampal CA3 Interneuron
categories: Tutorials
description: test description
---

Hippocampal CA3 Interneuron
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1 change: 0 additions & 1 deletion _pages/ImageJ1-ImageJ2_cheat_sheet.md
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autogenerated: true
title: ImageJ1-ImageJ2 cheat sheet
categories: Tutorials,Development
description: test description
---

This page summarizes translation of basic operations of ImageJ1 and ImageJ2 API. Based on the work of {%- include person id='haesleinhuepf' -%}, Scientific Computing Facility, MPI-CBG Dresden.
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1 change: 0 additions & 1 deletion _pages/ImageJ2_Documentation_Edit_Options_Compatibility.md
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autogenerated: true
title: ImageJ2/Documentation/Edit/Options/Compatibility
categories: software
description: test description
---

This page documents the {% include bc path='Edit | Options | Compatibility'%} command dialog.
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autogenerated: true
title: ImageJ2/Documentation/Image/Overlay/OverlayManager
categories: software
description: test description
---

ImageJ2's Overlay Manager is fairly similar to the ImageJ 1.x ROI Manager. See the [ImageJ 1.x documentation of its ROI Manager](/ij/docs/menus/analyze.html#manager).
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1 change: 0 additions & 1 deletion _pages/ImageJ2_Documentation_PointSetDemo.md
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---
autogenerated: true
title: ImageJ2/Documentation/PointSetDemo
description: test description
---

This page documents the language used in the PointSet Demo plugin.
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1 change: 0 additions & 1 deletion _pages/ImageJ2_Documentation_Process_Math_Equation.md
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---
autogenerated: true
title: ImageJ2/Documentation/Process/Math/Equation
description: test description
---

This page documents that language that can be used to specify equations via the {% include bc path='Process | Math | Equation'%} command.
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1 change: 0 additions & 1 deletion _pages/ImageJ2_development_releases.md
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autogenerated: true
title: ImageJ2 development releases
categories: sofware
description: test description
---

This table lists the versions of [ImageJ2](/software/imagej2) released during its initial incubation period.
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1 change: 0 additions & 1 deletion _pages/ImageJ2_grant_proposal.md
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---
autogenerated: true
title: ImageJ2 grant proposal
description: test description
---

The following is the original text of the [ImageJDev](/software/imagej2) grant proposal circa mid-2009. {% include warning-box message='Please note that [ImageJ2](/software/imagej2)"s project directions evolved substantially as it developed, so the text below is dated, but in many ways, this document continues to represent the project"s conceptual core.' %}
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1 change: 0 additions & 1 deletion _pages/ImgLibProcessor.md
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autogenerated: true
title: ImgLibProcessor
categories: ImageJ2,Development
description: test description
---

{% include warning-box content='The following article describes a method of ImageJ1/ImageJ2 integration we explored in 2010, revolving around an `ij.process.ImageProcessor` extension called `ImgLibProcessor` which would enable additional transparent usage of [ImgLib2](/imglib2) from within ImageJ1, thus greatly expanding the available pixel types and storage strategies. However, after discussion with [Wayne Rasband](/users/rasband), we settled on a different method of backwards compatibility known as [ImageJ Legacy](/libs/imagej-legacy). The text below is preserved only for historical reasons.' %}
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1 change: 0 additions & 1 deletion _pages/Imprint.md
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---
autogenerated: true
title: Imprint
description: test description
---

The ImageJ Wiki is hosted at the [Laboratory for Optical and Computational Instrumentation (LOCI)](http://loci.wisc.edu/) of the University of Wisconsin-Madison.
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1 change: 0 additions & 1 deletion _pages/Installing_3rd_party_plugins.md
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autogenerated: true
title: Installing 3rd party plugins
categories: Tutorials
description: test description
---

For users
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1 change: 0 additions & 1 deletion _pages/Java_Options.md
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autogenerated: true
title: Java Options
categories: development
description: test description
---

Introduction
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1 change: 0 additions & 1 deletion _pages/Java_Tricks_and_Quirks.md
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autogenerated: true
title: Java Tricks and Quirks
categories: development
description: test description
---

SoftReference and OutOfMemoryError
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1 change: 0 additions & 1 deletion _pages/Keyboard_shortcuts.md
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autogenerated: true
title: Keyboard shortcuts
categories: User interface, tutorials
description: test description
---


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1 change: 0 additions & 1 deletion _pages/Launcher.md
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---
autogenerated: true
title: Launcher
description: test description
---

The ImageJ launcher is a native application for launching ImageJ.
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1 change: 0 additions & 1 deletion _pages/Linux_command_line_tutorial.md
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autogenerated: true
title: Linux command line tutorial
categories: tutorials
description: test description
---

Connecting to the cluster
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1 change: 0 additions & 1 deletion _pages/Mamed.md
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autogenerated: true
title: Mamed
categories: Tutorials
description: test description
---

Mamed
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1 change: 0 additions & 1 deletion _pages/Metadata.md
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---
autogenerated: true
title: Metadata
description: test description
---

What is metadata?
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1 change: 0 additions & 1 deletion _pages/Open_Source.md
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autogenerated: true
title: Open Source
categories: Development
description: test description
---

![ 64px \| left \| link=https://opensource.org/](/media/Osi symbol.png "fig: 64px | left | link=https://opensource.org/") The [ImageJ](/about) project, and related projects in the [SciJava](SciJava) software ecosystem, are open source software projects. See the [Licensing](/licensing) page for details.
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1 change: 0 additions & 1 deletion _pages/Open_an_image.md
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autogenerated: true
title: Open an image
categories: tutorials
description: test description
---

**How to open an image in ImageJ2?**
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1 change: 0 additions & 1 deletion _pages/Project_ideas.md
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autogenerated: true
title: Project ideas
categories: development
description: test description
---

This page contains a loose list of ideas for cool/useful projects that have some relation to Fiji
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1 change: 0 additions & 1 deletion _pages/SciJava.md
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autogenerated: true
title: SciJava
categories: development
description: test description
---

{% include project content='SciJava' %}
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1 change: 0 additions & 1 deletion _pages/Skeleton_analysis_video_tutorial.md
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autogenerated: true
title: Skeleton analysis video tutorial
categories: Tutorials
description: test description
---

TODO FLASH WIDGET
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1 change: 0 additions & 1 deletion _pages/TaskList.md
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autogenerated: true
title: TaskList
categories: Hackathons, community
description: test description
---

This is the summary of the final project meeting of the [Hackathon](/events/Hackathon) which took place at the MPI-CBG in Dresden/Germany from 04/21/2008 till 04/30/2008.
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1 change: 0 additions & 1 deletion _pages/Why_Closed-Source_Is_Wrong.md
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autogenerated: true
title: Why Closed-Source Is Wrong
categories: development
description: test description
---

This page has a few war stories about having to fight with developing software where you should not need to fight.
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1 change: 0 additions & 1 deletion _pages/about/chat.md
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autogenerated: true
title: Chat
categories: Help
description: test description
---

[ImageJ](/about) community members are often available via a couple of different chat services.
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1 change: 0 additions & 1 deletion _pages/about/citing.md
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autogenerated: true
title: Citing
section: About
description: test description
---

{% include info-box content='This page describes how to *cite* [SciJava](SciJava) projects.
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1 change: 0 additions & 1 deletion _pages/about/contributing.md
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title: Contributing
section: About
categories: community
description: test description
---


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1 change: 0 additions & 1 deletion _pages/about/contributors.md
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title: Contributors
section: About
categories: community
description: test description
---

{% include info-box content='This page describes who *contributes* to [SciJava](SciJava) projects.
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1 change: 0 additions & 1 deletion _pages/about/debian.md
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---
autogenerated: true
title: Debian
description: test description
---

The [Fiji](/fiji) project used to offer Debian packages. Unfortunately, for a variety of reasons, we are withdrawing support for these packages until such time as someone is able to maintain them properly, so please switch to using the Linux downloads on the [ImageJ /downloads](/downloads) and [Fiji /downloads](/fiji/downloads) pages instead.
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1 change: 0 additions & 1 deletion _pages/about/funding.md
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autogenerated: true
title: Funding
section: About
description: test description
---

{% include info-box content='This page describes *how* [SciJava](SciJava) projects are funded.
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1 change: 0 additions & 1 deletion _pages/about/governance.md
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title: Governance
section: About
categories: Development
description: test description
---

{% include info-box content='This page describes the *social* structure of [SciJava](SciJava) projects.
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1 change: 0 additions & 1 deletion _pages/about/index.md
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title: ImageJ
section: About
categories: Citable,Software
description: test description
---


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1 change: 0 additions & 1 deletion _pages/about/mailing-lists.md
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autogenerated: true
title: Mailing Lists
categories: community
description: test description
---

There are several mailing lists for community discussion and troubleshooting.{% include recommendedcontact%}
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1 change: 0 additions & 1 deletion _pages/about/usage.md
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autogenerated: true
title: Usage
section: About
description: test description
---


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