The best way to collect debugging information is to build the site locally. However if that isn’t an option, this page documents tags which can be helpful.

Echo

This echo include just prints its arguments, for debugging/learning purposes. This can be helpful in understanding Liquid syntax and how strings are being read internally by an include.

Arguments are printed as a comma-separated list of "argument"==>"value" pairs.

Note that liquid allows the passing of arbitrary arguments to include templates. All these arguments will be stored, but won’t have any effect unless the include’s source actually does something with those arguments.

{% include echo content="This is the content argument" bracket="what if I pass {}?" gorilla="Why do we have a gorilla argument?" %}

{"content"=>"This is the content argument", "bracket"=>"what if I pass {}?", "gorilla"=>"Why do we have a gorilla argument?"}

What’s in a page?

Ever wonder what all is part of the page data structure? Let’s find out!

(You can also do this with the site data structure, but be warned: the output will include every page body across the whole site!)

{% include echo p=page %}

{"p"=>{ "path": "_pages/editing/debugging.md", "relative_path": "_pages/editing/debugging.md", "excerpt": "

The best way to collect debugging information is to <a href=\"/editing/advanced\">build the site locally</a>. However if that isn’t an option, this page documents tags which can be helpful.

This page describes nice ways of embedding source code in a page.

This page demonstrates how to add a citation to your page.

μManager Documentation

\n
• <a href=\"/news/index\">News</a>
\n\n\n
• <a href=\"/Download_Micro-Manager_Latest_Release\">Downloads</a>

  \n
  • <a href=\"/Micro-Manager_Nightly_Builds\">Nightly Builds</a>
  \n
  • <a href=\"/Micro-Manager_Version_Archive\">Old Releases</a>
  \n
  • <a href=\"/Micro-Manager_Installation_Notes\">Installation Notes</a>
  \n
  • <a href=\"/Micro-Manager_Source_Code\">Source Code</a>
  \n

  \n
  \n
\n\n\n\n
• <a href=\"/Micro-Manager_Project_Overview\">Learn</a>

  \n \n
  • <a href=\"/Micro-Manager_Project_Overview\">Overview</a>

    \n
    • <a href=\"/Why_Micro-Manager\">Why Micro-Manager?</a>
    \n
    • <a href=\"/Who_should_use_Micro-Manager\">Who should use Micro-Manager</a>
    \n

    \n
    \n
  \n\n\n \n
  • <a href=\"/Version_2.0\">Version 2.0</a>

    \n
    • <a href=\"/Version_2.0_Users_Guide\">User Guide</a>
    \n
    • <a href=\"/Micro-Manager_Configuration_Guide\">Hardware Configuration Guide</a>
    \n
    • <a href=\"/Version_2.0_Plugins\">Plugins</a>
    \n
    • <a href=\"/Version_2.0_FAQ\">FAQ</a>
    \n
    • <a href=\"/Version_2.0_More_Help_Topics\">More Help Topics</a>
    \n
    • <a href=\"/Version_2.0_API\">API</a>
    \n
    • <a href=\"/Version_2.0_API_Transition_Guide\">API Transition Guide</a>
    \n
    • <a href=\"/Version_2.0_API_How_do_I\">API, How do I?</a>
    \n
    • <a href=\"/apidoc/mmstudio/latest/org/micromanager/Studio.html\">Javadoc</a>
    \n
    • <a href=\"/Version_2.0_API_Events\">API Events</a>
    \n
    • <a href=\"/Version_2.0_Plugins\">Writing Plugins</a>
    \n
    • <a href=\"/Version_2.0_Scripts\">Scripting</a>
    \n

    \n
    \n
  \n\n\n \n
  • <a href=\"/Overview_of_the_documentation\">Version 1.4</a>

    \n
    • <a href=\"/Micro-Manager_User's_Guide\">User Guide</a>
    \n
    • <a href=\"/Micro-Manager_Configuration_Guide\">Hardware Configuration Guide</a>
    \n
    • <a href=\"/Plugins\">Plugins</a>
    \n
    • <a href=\"http://valelab4.ucsf.edu/publications/2010EdelsteinCurrProt.pdf\">Tutorial (PDF)</a>
    \n
    • <a href=\"http://www.jbmethods.org/jbm/article/view/36/29\">Advanced Methods</a>
    \n
    • <a href=\"/Micro-Manager_FAQ-new\">FAQ</a>
    \n
    • <a href=\"/More_Help_Topics\">More Help Topics</a>
    \n
    • <a href=\"/Screencasts\">Video Screencasts</a>
    \n

    \n
    \n
  \n\n

  \n
  \n
\n\n\n\n
• <a href=\"/Micro-Manager_Programming_Guide\">Extend</a>

  \n
  • <a href=\"/Script_Panel_GUI\">Scripting (Beanshell)</a>
  \n
  • <a href=\"/Example_Beanshell_scripts\">Example Beanshell scripts</a>
  \n
  • <a href=\"/Writing_plugins_for_Micro-Manager\">Writing Plugins</a>
  \n
  • <a href=\"/Using_the_Micro-Manager_python_library\">Python</a>
  \n
  • <a href=\"/Matlab\">Matlab</a>
  \n
  • <a href=\"/Micro-Manager_File_Formats\">File Formats</a>
  \n
  • <a href=\"/Search_Paths\">Search Paths</a>
  \n
  • <a href=\"/Building_Micro-Manager_Device_Adapters\">Writing Device Adapters</a>
  \n
  • <a href=\"/Free_third-party_tools_for_testing_communications_with_hardware\">Testing communication with hardware</a>
  \n
  • <a href=\"/Building_and_debugging_Micro-Manager_source_code\">Building and Debugging Micro-Manager</a>
  \n
  • <a href=\"/Multi-Dimensional_Acquisition_Programming\">Multi-D Acq. Programming</a>
  \n
  • <a href=\"/Policies_for_inclusion_of_source_code\">Policies for inclusion of source code</a>
  \n
  • <a href=\"https://github.com/micro-manager\">Source code repository history and tickets</a>
  \n
  • APIs

    \n
    • <a href=\"/apidoc/mmstudio/latest/org/micromanager/Studio.html\">2.0 MMStudio API Reference (Java/Beanshell)</a>
    \n
    • <a href=\"/apidoc/mmstudio/1.4/org/micromanager/api/ScriptInterface.html\">1.4 MMStudio API Reference (Java/Beanshell)</a>
    \n
    • <a href=\"/apidoc/mmcorej/latest/mmcorej/CMMCore.html\">Core API Reference (Java/Beanshell)</a>
    \n
    • <a href=\"/apidoc/MMCore/latest/class_c_m_m_core.html\">Core API Reference (C++)</a>
    \n
    • <a href=\"/apidoc/MMDevice/latest/class_m_m_1_1_device.html\">Device API Reference (C++)</a>
    \n

    \n
    \n
  \n\n

  \n
  \n
\n\n\n\n
• <a href=\"/Device_Support\">Devices</a>

  \n
  • <a href=\"/Micro-Manager_Configuration_Guide\">Hardware Configuration Guide</a>
  \n

  \n
  \n
\n\n\n\n
• <a href=\"/Micro-Manager_Community\">Support</a>

  \n
  • <a href=\"/Contact\">Contact</a>
  \n
  • <a href=\"/System_Integrators\">System Integrators</a>
  \n
  • <a href=\"/Programming_Services\">Programming Services</a>
  \n
  • <a href=\"/editing/\">Editing the Wiki</a>

    \n
    • <a href=\"/editing/advanced\">Advanced editing</a>
    \n
    • <a href=\"/editing/buttons\">Buttons</a>
    \n
    • <a class=\"current-page\">Citations</a>
    \n
    • <a href=\"/editing/code\">Source Code</a>
    \n
    • <a href=\"/editing/headers\">Headers</a>
    \n
    • <a href=\"/editing/icons\">Icons</a>
    \n
    • <a href=\"/editing/images\">Images</a>
    \n
    • <a href=\"/editing/keys\">Keyboard Shortcuts</a>
    \n
    • <a href=\"/editing/linking\">Linking</a>
    \n
    • <a href=\"/editing/math\">Math Expressions</a>
    \n
    • <a href=\"/editing/notices\">Notices</a>
    \n
    • <a href=\"/editing/pitfalls\">Pitfalls</a>
    \n
    • <a href=\"/editing/symbols\">Symbols</a>
    \n
    • <a href=\"/editing/tables\">Tables</a>
    \n
    • <a href=\"/editing/videos\">Videos</a>
    \n
    • <a href=\"/editing/whitespace\">Whitespace</a>
    \n

    \n
    \n
  \n \n

  \n
  \n
\n\n\n\n
• <a href=\"/Credits\">Credits</a>

  \n
  • <a href=\"/Papers_citing_Micro-Manager\">Papers citing MicroManager</a>
  \n
  • <a href=\"/Citing_Micro-Manager\">How to cite MicroManager</a>
  \n

  \n
  \n
\n\n\n

Citations

Page contents

This page demonstrates how to add a citation to your page.

<code class=\"language-plaintext highlighter-rouge\">include citation</code> allows you to create a single-use citation, or footnote.

This include creates a citation given the following inputs:\nauthor (all authors of the publication, this input will be presented as entered):

\ntitle title of the publication
\nurl url link to location the publication is hosted
\nyear year of publication
\njournal name of the publishing journal
\nvolume volume of the publishing journal
\nnumber issuing number of the publishing journal
\npages page numbers that the publication appears in publishing journal
\ndoi digital object identifier
\nfn foot note number

The following liquid code:

produces:

Albert Cardona, Stephan Saalfeld, Johannes Schindelin, Ignacio Arganda-Carreras, Stephan Preibisch, Mark Longair, Pavel Tomancak, Volker Hartenstein and Rodney J. Douglas (2012), “<a href=\"http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038011\">TrakEM2 software for neural circuit reconstruction</a>”, PLoS ONE , doi:<a href=\"https://dx.doi.org/10.1371/journal.pone.0038011\">10.1371/journal.pone.0038011</a>.

Use the <a href=\"https://kramdown.gettalong.org/quickref.html#footnotes\">kramdown syntax</a> in your document to refer to footnotes by number.

NB: regardless of where the liquid reference appears in your document, footnote text will always be at the bottom.

Specify the footnote number in the <code class=\"language-plaintext highlighter-rouge\">include</code>.

The following markdown and liquid code:

produces:

This is a reference<sup id=\"fnref:1\" role=\"doc-noteref\"><a href=\"#fn:1\" class=\"footnote\" rel=\"footnote\">1</a></sup>.

\n <li id=\"fn:1\" role=\"doc-endnote\">\n

Albert Cardona, Stephan Saalfeld, Johannes Schindelin, Ignacio Arganda-Carreras, Stephan Preibisch, Mark Longair, Pavel Tomancak, Volker Hartenstein and Rodney J. Douglas (2012), “<a href=\"http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038011\">TrakEM2 software for neural circuit reconstruction</a>”, PLoS ONE , doi:<a href=\"https://dx.doi.org/10.1371/journal.pone.0038011\">10.1371/journal.pone.0038011</a>. <a href=\"#fnref:1\" class=\"reversefootnote\" role=\"doc-backlink\">↩</a>

\n </li>\n

μManager Documentation

\n
• <a href=\"/news/index\">News</a>
\n\n\n
• <a href=\"/Download_Micro-Manager_Latest_Release\">Downloads</a>

  \n
  • <a href=\"/Micro-Manager_Nightly_Builds\">Nightly Builds</a>
  \n
  • <a href=\"/Micro-Manager_Version_Archive\">Old Releases</a>
  \n
  • <a href=\"/Micro-Manager_Installation_Notes\">Installation Notes</a>
  \n
  • <a href=\"/Micro-Manager_Source_Code\">Source Code</a>
  \n

  \n
  \n
\n\n\n\n
• <a href=\"/Micro-Manager_Project_Overview\">Learn</a>

  \n \n
  • <a href=\"/Micro-Manager_Project_Overview\">Overview</a>

    \n
    • <a href=\"/Why_Micro-Manager\">Why Micro-Manager?</a>
    \n
    • <a href=\"/Who_should_use_Micro-Manager\">Who should use Micro-Manager</a>
    \n

    \n
    \n
  \n\n\n \n
  • <a href=\"/Version_2.0\">Version 2.0</a>

    \n
    • <a href=\"/Version_2.0_Users_Guide\">User Guide</a>
    \n
    • <a href=\"/Micro-Manager_Configuration_Guide\">Hardware Configuration Guide</a>
    \n
    • <a href=\"/Version_2.0_Plugins\">Plugins</a>
    \n
    • <a href=\"/Version_2.0_FAQ\">FAQ</a>
    \n
    • <a href=\"/Version_2.0_More_Help_Topics\">More Help Topics</a>
    \n
    • <a href=\"/Version_2.0_API\">API</a>
    \n
    • <a href=\"/Version_2.0_API_Transition_Guide\">API Transition Guide</a>
    \n
    • <a href=\"/Version_2.0_API_How_do_I\">API, How do I?</a>
    \n
    • <a href=\"/apidoc/mmstudio/latest/org/micromanager/Studio.html\">Javadoc</a>
    \n
    • <a href=\"/Version_2.0_API_Events\">API Events</a>
    \n
    • <a href=\"/Version_2.0_Plugins\">Writing Plugins</a>
    \n
    • <a href=\"/Version_2.0_Scripts\">Scripting</a>
    \n

    \n
    \n
  \n\n\n \n
  • <a href=\"/Overview_of_the_documentation\">Version 1.4</a>

    \n
    • <a href=\"/Micro-Manager_User's_Guide\">User Guide</a>
    \n
    • <a href=\"/Micro-Manager_Configuration_Guide\">Hardware Configuration Guide</a>
    \n
    • <a href=\"/Plugins\">Plugins</a>
    \n
    • <a href=\"http://valelab4.ucsf.edu/publications/2010EdelsteinCurrProt.pdf\">Tutorial (PDF)</a>
    \n
    • <a href=\"http://www.jbmethods.org/jbm/article/view/36/29\">Advanced Methods</a>
    \n
    • <a href=\"/Micro-Manager_FAQ-new\">FAQ</a>
    \n
    • <a href=\"/More_Help_Topics\">More Help Topics</a>
    \n
    • <a href=\"/Screencasts\">Video Screencasts</a>
    \n

    \n
    \n
  \n\n

  \n
  \n
\n\n\n\n
• <a href=\"/Micro-Manager_Programming_Guide\">Extend</a>

  \n
  • <a href=\"/Script_Panel_GUI\">Scripting (Beanshell)</a>
  \n
  • <a href=\"/Example_Beanshell_scripts\">Example Beanshell scripts</a>
  \n
  • <a href=\"/Writing_plugins_for_Micro-Manager\">Writing Plugins</a>
  \n
  • <a href=\"/Using_the_Micro-Manager_python_library\">Python</a>
  \n
  • <a href=\"/Matlab\">Matlab</a>
  \n
  • <a href=\"/Micro-Manager_File_Formats\">File Formats</a>
  \n
  • <a href=\"/Search_Paths\">Search Paths</a>
  \n
  • <a href=\"/Building_Micro-Manager_Device_Adapters\">Writing Device Adapters</a>
  \n
  • <a href=\"/Free_third-party_tools_for_testing_communications_with_hardware\">Testing communication with hardware</a>
  \n
  • <a href=\"/Building_and_debugging_Micro-Manager_source_code\">Building and Debugging Micro-Manager</a>
  \n
  • <a href=\"/Multi-Dimensional_Acquisition_Programming\">Multi-D Acq. Programming</a>
  \n
  • <a href=\"/Policies_for_inclusion_of_source_code\">Policies for inclusion of source code</a>
  \n
  • <a href=\"https://github.com/micro-manager\">Source code repository history and tickets</a>
  \n
  • APIs

    \n
    • <a href=\"/apidoc/mmstudio/latest/org/micromanager/Studio.html\">2.0 MMStudio API Reference (Java/Beanshell)</a>
    \n
    • <a href=\"/apidoc/mmstudio/1.4/org/micromanager/api/ScriptInterface.html\">1.4 MMStudio API Reference (Java/Beanshell)</a>
    \n
    • <a href=\"/apidoc/mmcorej/latest/mmcorej/CMMCore.html\">Core API Reference (Java/Beanshell)</a>
    \n
    • <a href=\"/apidoc/MMCore/latest/class_c_m_m_core.html\">Core API Reference (C++)</a>
    \n
    • <a href=\"/apidoc/MMDevice/latest/class_m_m_1_1_device.html\">Device API Reference (C++)</a>
    \n

    \n
    \n
  \n\n

  \n
  \n
\n\n\n\n
• <a href=\"/Device_Support\">Devices</a>

  \n
  • <a href=\"/Micro-Manager_Configuration_Guide\">Hardware Configuration Guide</a>
  \n

  \n
  \n
\n\n\n\n
• <a href=\"/Micro-Manager_Community\">Support</a>

  \n
  • <a href=\"/Contact\">Contact</a>
  \n
  • <a href=\"/System_Integrators\">System Integrators</a>
  \n
  • <a href=\"/Programming_Services\">Programming Services</a>
  \n
  • <a href=\"/editing/\">Editing the Wiki</a>

    \n
    • <a href=\"/editing/advanced\">Advanced editing</a>
    \n
    • <a href=\"/editing/buttons\">Buttons</a>
    \n
    • <a class=\"current-page\">Citations</a>
    \n
    • <a href=\"/editing/code\">Source Code</a>
    \n
    • <a href=\"/editing/headers\">Headers</a>
    \n
    • <a href=\"/editing/icons\">Icons</a>
    \n
    • <a href=\"/editing/images\">Images</a>
    \n
    • <a href=\"/editing/keys\">Keyboard Shortcuts</a>
    \n
    • <a href=\"/editing/linking\">Linking</a>
    \n
    • <a href=\"/editing/math\">Math Expressions</a>
    \n
    • <a href=\"/editing/notices\">Notices</a>
    \n
    • <a href=\"/editing/pitfalls\">Pitfalls</a>
    \n
    • <a href=\"/editing/symbols\">Symbols</a>
    \n
    • <a href=\"/editing/tables\">Tables</a>
    \n
    • <a href=\"/editing/videos\">Videos</a>
    \n
    • <a href=\"/editing/whitespace\">Whitespace</a>
    \n

    \n
    \n
  \n \n

  \n
  \n
\n\n\n\n
• <a href=\"/Credits\">Credits</a>

  \n
  • <a href=\"/Papers_citing_Micro-Manager\">Papers citing MicroManager</a>
  \n
  • <a href=\"/Citing_Micro-Manager\">How to cite MicroManager</a>
  \n

  \n
  \n
\n\n\n

This page demonstrates how to add a citation to your page.

<code class=\"language-plaintext highlighter-rouge\">include citation</code> allows you to create a single-use citation, or footnote.

This include creates a citation given the following inputs:\nauthor (all authors of the publication, this input will be presented as entered):

\ntitle title of the publication
\nurl url link to location the publication is hosted
\nyear year of publication
\njournal name of the publishing journal
\nvolume volume of the publishing journal
\nnumber issuing number of the publishing journal
\npages page numbers that the publication appears in publishing journal
\ndoi digital object identifier
\nfn foot note number

The following liquid code:

produces:

Albert Cardona, Stephan Saalfeld, Johannes Schindelin, Ignacio Arganda-Carreras, Stephan Preibisch, Mark Longair, Pavel Tomancak, Volker Hartenstein and Rodney J. Douglas (2012), “<a href=\"http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038011\">TrakEM2 software for neural circuit reconstruction</a>”, PLoS ONE , doi:<a href=\"https://dx.doi.org/10.1371/journal.pone.0038011\">10.1371/journal.pone.0038011</a>.

Use the <a href=\"https://kramdown.gettalong.org/quickref.html#footnotes\">kramdown syntax</a> in your document to refer to footnotes by number.

NB: regardless of where the liquid reference appears in your document, footnote text will always be at the bottom.

Specify the footnote number in the <code class=\"language-plaintext highlighter-rouge\">include</code>.

The following markdown and liquid code:

produces:

This is a reference<sup id=\"fnref:1\" role=\"doc-noteref\"><a href=\"#fn:1\" class=\"footnote\" rel=\"footnote\">1</a></sup>.

\n <li id=\"fn:1\" role=\"doc-endnote\">\n

Albert Cardona, Stephan Saalfeld, Johannes Schindelin, Ignacio Arganda-Carreras, Stephan Preibisch, Mark Longair, Pavel Tomancak, Volker Hartenstein and Rodney J. Douglas (2012), “<a href=\"http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038011\">TrakEM2 software for neural circuit reconstruction</a>”, PLoS ONE , doi:<a href=\"https://dx.doi.org/10.1371/journal.pone.0038011\">10.1371/journal.pone.0038011</a>. <a href=\"#fnref:1\" class=\"reversefootnote\" role=\"doc-backlink\">↩</a>

\n </li>\n

The best way to collect debugging information is to <a href=\"/editing/advanced\">build the site locally</a>. However if that isn’t an option, this page documents tags which can be helpful.

μManager Documentation

\n
• <a href=\"/news/index\">News</a>
\n\n\n
• <a href=\"/Download_Micro-Manager_Latest_Release\">Downloads</a>

  \n
  • <a href=\"/Micro-Manager_Nightly_Builds\">Nightly Builds</a>
  \n
  • <a href=\"/Micro-Manager_Version_Archive\">Old Releases</a>
  \n
  • <a href=\"/Micro-Manager_Installation_Notes\">Installation Notes</a>
  \n
  • <a href=\"/Micro-Manager_Source_Code\">Source Code</a>
  \n

  \n
  \n
\n\n\n\n
• <a href=\"/Micro-Manager_Project_Overview\">Learn</a>

  \n \n
  • <a href=\"/Micro-Manager_Project_Overview\">Overview</a>

    \n
    • <a href=\"/Why_Micro-Manager\">Why Micro-Manager?</a>
    \n
    • <a href=\"/Who_should_use_Micro-Manager\">Who should use Micro-Manager</a>
    \n

    \n
    \n
  \n\n\n \n
  • <a href=\"/Version_2.0\">Version 2.0</a>

    \n
    • <a href=\"/Version_2.0_Users_Guide\">User Guide</a>
    \n
    • <a href=\"/Micro-Manager_Configuration_Guide\">Hardware Configuration Guide</a>
    \n
    • <a href=\"/Version_2.0_Plugins\">Plugins</a>
    \n
    • <a href=\"/Version_2.0_FAQ\">FAQ</a>
    \n
    • <a href=\"/Version_2.0_More_Help_Topics\">More Help Topics</a>
    \n
    • <a href=\"/Version_2.0_API\">API</a>
    \n
    • <a href=\"/Version_2.0_API_Transition_Guide\">API Transition Guide</a>
    \n
    • <a href=\"/Version_2.0_API_How_do_I\">API, How do I?</a>
    \n
    • <a href=\"/apidoc/mmstudio/latest/org/micromanager/Studio.html\">Javadoc</a>
    \n
    • <a href=\"/Version_2.0_API_Events\">API Events</a>
    \n
    • <a href=\"/Version_2.0_Plugins\">Writing Plugins</a>
    \n
    • <a href=\"/Version_2.0_Scripts\">Scripting</a>
    \n

    \n
    \n
  \n\n\n \n
  • <a href=\"/Overview_of_the_documentation\">Version 1.4</a>

    \n
    • <a href=\"/Micro-Manager_User's_Guide\">User Guide</a>
    \n
    • <a href=\"/Micro-Manager_Configuration_Guide\">Hardware Configuration Guide</a>
    \n
    • <a href=\"/Plugins\">Plugins</a>
    \n
    • <a href=\"http://valelab4.ucsf.edu/publications/2010EdelsteinCurrProt.pdf\">Tutorial (PDF)</a>
    \n
    • <a href=\"http://www.jbmethods.org/jbm/article/view/36/29\">Advanced Methods</a>
    \n
    • <a href=\"/Micro-Manager_FAQ-new\">FAQ</a>
    \n
    • <a href=\"/More_Help_Topics\">More Help Topics</a>
    \n
    • <a href=\"/Screencasts\">Video Screencasts</a>
    \n

    \n
    \n
  \n\n

  \n
  \n
\n\n\n\n
• <a href=\"/Micro-Manager_Programming_Guide\">Extend</a>

  \n
  • <a href=\"/Script_Panel_GUI\">Scripting (Beanshell)</a>
  \n
  • <a href=\"/Example_Beanshell_scripts\">Example Beanshell scripts</a>
  \n
  • <a href=\"/Writing_plugins_for_Micro-Manager\">Writing Plugins</a>
  \n
  • <a href=\"/Using_the_Micro-Manager_python_library\">Python</a>
  \n
  • <a href=\"/Matlab\">Matlab</a>
  \n
  • <a href=\"/Micro-Manager_File_Formats\">File Formats</a>
  \n
  • <a href=\"/Search_Paths\">Search Paths</a>
  \n
  • <a href=\"/Building_Micro-Manager_Device_Adapters\">Writing Device Adapters</a>
  \n
  • <a href=\"/Free_third-party_tools_for_testing_communications_with_hardware\">Testing communication with hardware</a>
  \n
  • <a href=\"/Building_and_debugging_Micro-Manager_source_code\">Building and Debugging Micro-Manager</a>
  \n
  • <a href=\"/Multi-Dimensional_Acquisition_Programming\">Multi-D Acq. Programming</a>
  \n
  • <a href=\"/Policies_for_inclusion_of_source_code\">Policies for inclusion of source code</a>
  \n
  • <a href=\"https://github.com/micro-manager\">Source code repository history and tickets</a>
  \n
  • APIs

    \n
    • <a href=\"/apidoc/mmstudio/latest/org/micromanager/Studio.html\">2.0 MMStudio API Reference (Java/Beanshell)</a>
    \n
    • <a href=\"/apidoc/mmstudio/1.4/org/micromanager/api/ScriptInterface.html\">1.4 MMStudio API Reference (Java/Beanshell)</a>
    \n
    • <a href=\"/apidoc/mmcorej/latest/mmcorej/CMMCore.html\">Core API Reference (Java/Beanshell)</a>
    \n
    • <a href=\"/apidoc/MMCore/latest/class_c_m_m_core.html\">Core API Reference (C++)</a>
    \n
    • <a href=\"/apidoc/MMDevice/latest/class_m_m_1_1_device.html\">Device API Reference (C++)</a>
    \n

    \n
    \n
  \n\n

  \n
  \n
\n\n\n\n
• <a href=\"/Device_Support\">Devices</a>

  \n
  • <a href=\"/Micro-Manager_Configuration_Guide\">Hardware Configuration Guide</a>
  \n

  \n
  \n
\n\n\n\n
• <a href=\"/Micro-Manager_Community\">Support</a>

  \n
  • <a href=\"/Contact\">Contact</a>
  \n
  • <a href=\"/System_Integrators\">System Integrators</a>
  \n
  • <a href=\"/Programming_Services\">Programming Services</a>
  \n
  • <a href=\"/editing/\">Editing the Wiki</a>

    \n
    • <a href=\"/editing/advanced\">Advanced editing</a>
    \n
    • <a href=\"/editing/buttons\">Buttons</a>
    \n
    • <a href=\"/editing/citations\">Citations</a>
    \n
    • <a class=\"current-page\">Source Code</a>
    \n
    • <a href=\"/editing/headers\">Headers</a>
    \n
    • <a href=\"/editing/icons\">Icons</a>
    \n
    • <a href=\"/editing/images\">Images</a>
    \n
    • <a href=\"/editing/keys\">Keyboard Shortcuts</a>
    \n
    • <a href=\"/editing/linking\">Linking</a>
    \n
    • <a href=\"/editing/math\">Math Expressions</a>
    \n
    • <a href=\"/editing/notices\">Notices</a>
    \n
    • <a href=\"/editing/pitfalls\">Pitfalls</a>
    \n
    • <a href=\"/editing/symbols\">Symbols</a>
    \n
    • <a href=\"/editing/tables\">Tables</a>
    \n
    • <a href=\"/editing/videos\">Videos</a>
    \n
    • <a href=\"/editing/whitespace\">Whitespace</a>
    \n

    \n
    \n
  \n \n

  \n
  \n
\n\n\n\n
• <a href=\"/Credits\">Credits</a>

  \n
  • <a href=\"/Papers_citing_Micro-Manager\">Papers citing MicroManager</a>
  \n
  • <a href=\"/Citing_Micro-Manager\">How to cite MicroManager</a>
  \n

  \n
  \n
\n\n\n

Source Code

Page contents

This page describes nice ways of embedding source code in a page.

If you just want to write a short snippet of code as part of a sentence,\nsurround the code in backtick symbols (`).

<code class=\"language-liquid\" data-lang=\"liquid\">Type `print('Hello world!')` and save as `hello.py`.</code>

A “code fence” is three backtick symbols (```) preceding your\ncode, and another three concluding it. Optionally, you can write the name of\nthe language in small case next to the leading fence to declare syntax\nhighlighting is desired with the stated language.

<code class=\"language-liquid\" data-lang=\"liquid\">```java\nImage3DUniverse univ = new Image3DUniverse();\nuniv.show();\nuniv.addMesh(yourImagePlus, null, \"somename\", 50,\n  new boolean[] {true, true, true}, 2);\n```</code>

<code class=\"language-liquid\" data-lang=\"liquid\">```python\ndef update_progress(progress):\n    barLength = 10 # length of progress bar\n    block = int(round(barLength*progress))\n    text = f'\\rPercent complete: ' +\n      f'[{\"#\"*block + \"-\"*(barLength-block)}] ' +\n      f'{progress*100}%'\n    sys.stdout.write(text)\n    sys.stdout.flush()\n```</code>

Alternately, there is a <code class=\"language-plaintext highlighter-rouge\">highlight</code> Liquid directive you can try.\nIt looks like this:

<code class=\"language-liquid\" data-lang=\"liquid\"><span class=\"p\">{%</span><span class=\"w\"> </span><span class=\"nt\">highlight</span><span class=\"w\"> </span>java<span class=\"w\"> </span><span class=\"p\">%}</span>\nlog.info(\"You're a wizard, Harry!\");\nlog.error(\"I'm a what?\");\n<span class=\"p\">{%</span><span class=\"w\"> </span><span class=\"nt\">endhighlight</span><span class=\"w\"> </span><span class=\"p\">%}</span></code>

<code class=\"language-java\" data-lang=\"java\"><span class=\"n\">log</span><span class=\"o\">.</span><span class=\"na\">info</span><span class=\"o\">(</span><span class=\"s\">\"You're a wizard, Harry!\"</span><span class=\"o\">);</span>\n<span class=\"n\">log</span><span class=\"o\">.</span><span class=\"na\">error</span><span class=\"o\">(</span><span class=\"s\">\"I'm a what?\"</span><span class=\"o\">);</span></code>

The <code class=\"language-plaintext highlighter-rouge\">highlight</code> directive and code fences are separate features, but\nfunctionally very similar. If code fences are not working as you like,\ngive the <code class=\"language-plaintext highlighter-rouge\">highlight</code> directive a try to see if it does any better.

If you have a block of code in a GitHub repository, you can embed it\ndynamically into the page using the <code class=\"language-plaintext highlighter-rouge\">github-embed</code> include. This approach has\nthe advantage of avoiding copy-paste skew as the code evolves over time.

<code class=\"language-liquid\" data-lang=\"liquid\"><span class=\"p\">{%</span><span class=\"w\"> </span><span class=\"nt\">include</span><span class=\"w\"> </span><span class=\"nv\">github-embed</span><span class=\"err\">\n</span><span class=\"w\">     </span><span class=\"na\">org</span><span class=\"o\">=</span><span class=\"s2\">\"duckythescientist\"</span><span class=\"err\">\n</span><span class=\"w\">     </span><span class=\"na\">repo</span><span class=\"o\">=</span><span class=\"s2\">\"obfuscatedLife\"</span><span class=\"err\">\n</span><span class=\"w\">     </span><span class=\"na\">branch</span><span class=\"o\">=</span><span class=\"s2\">\"original\"</span><span class=\"err\">\n</span><span class=\"w\">     </span><span class=\"na\">path</span><span class=\"o\">=</span><span class=\"s2\">\"life.c\"</span><span class=\"err\">\n</span><span class=\"w\">     </span><span class=\"na\">label</span><span class=\"o\">=</span><span class=\"s2\">\"Conway's Obfuscated Game of Life\"</span><span class=\"w\"> </span><span class=\"p\">%}</span></code>

Other parameters supported by the <code class=\"language-plaintext highlighter-rouge\">github-embed</code> include are:

* Valid style values are:

μManager Documentation

\n
• <a href=\"/news/index\">News</a>
\n\n\n
• <a href=\"/Download_Micro-Manager_Latest_Release\">Downloads</a>

  \n
  • <a href=\"/Micro-Manager_Nightly_Builds\">Nightly Builds</a>
  \n
  • <a href=\"/Micro-Manager_Version_Archive\">Old Releases</a>
  \n
  • <a href=\"/Micro-Manager_Installation_Notes\">Installation Notes</a>
  \n
  • <a href=\"/Micro-Manager_Source_Code\">Source Code</a>
  \n

  \n
  \n
\n\n\n\n
• <a href=\"/Micro-Manager_Project_Overview\">Learn</a>

  \n \n
  • <a href=\"/Micro-Manager_Project_Overview\">Overview</a>

    \n
    • <a href=\"/Why_Micro-Manager\">Why Micro-Manager?</a>
    \n
    • <a href=\"/Who_should_use_Micro-Manager\">Who should use Micro-Manager</a>
    \n

    \n
    \n
  \n\n\n \n
  • <a href=\"/Version_2.0\">Version 2.0</a>

    \n
    • <a href=\"/Version_2.0_Users_Guide\">User Guide</a>
    \n
    • <a href=\"/Micro-Manager_Configuration_Guide\">Hardware Configuration Guide</a>
    \n
    • <a href=\"/Version_2.0_Plugins\">Plugins</a>
    \n
    • <a href=\"/Version_2.0_FAQ\">FAQ</a>
    \n
    • <a href=\"/Version_2.0_More_Help_Topics\">More Help Topics</a>
    \n
    • <a href=\"/Version_2.0_API\">API</a>
    \n
    • <a href=\"/Version_2.0_API_Transition_Guide\">API Transition Guide</a>
    \n
    • <a href=\"/Version_2.0_API_How_do_I\">API, How do I?</a>
    \n
    • <a href=\"/apidoc/mmstudio/latest/org/micromanager/Studio.html\">Javadoc</a>
    \n
    • <a href=\"/Version_2.0_API_Events\">API Events</a>
    \n
    • <a href=\"/Version_2.0_Plugins\">Writing Plugins</a>
    \n
    • <a href=\"/Version_2.0_Scripts\">Scripting</a>
    \n

    \n
    \n
  \n\n\n \n
  • <a href=\"/Overview_of_the_documentation\">Version 1.4</a>

    \n
    • <a href=\"/Micro-Manager_User's_Guide\">User Guide</a>
    \n
    • <a href=\"/Micro-Manager_Configuration_Guide\">Hardware Configuration Guide</a>
    \n
    • <a href=\"/Plugins\">Plugins</a>
    \n
    • <a href=\"http://valelab4.ucsf.edu/publications/2010EdelsteinCurrProt.pdf\">Tutorial (PDF)</a>
    \n
    • <a href=\"http://www.jbmethods.org/jbm/article/view/36/29\">Advanced Methods</a>
    \n
    • <a href=\"/Micro-Manager_FAQ-new\">FAQ</a>
    \n
    • <a href=\"/More_Help_Topics\">More Help Topics</a>
    \n
    • <a href=\"/Screencasts\">Video Screencasts</a>
    \n

    \n
    \n
  \n\n

  \n
  \n
\n\n\n\n
• <a href=\"/Micro-Manager_Programming_Guide\">Extend</a>

  \n
  • <a href=\"/Script_Panel_GUI\">Scripting (Beanshell)</a>
  \n
  • <a href=\"/Example_Beanshell_scripts\">Example Beanshell scripts</a>
  \n
  • <a href=\"/Writing_plugins_for_Micro-Manager\">Writing Plugins</a>
  \n
  • <a href=\"/Using_the_Micro-Manager_python_library\">Python</a>
  \n
  • <a href=\"/Matlab\">Matlab</a>
  \n
  • <a href=\"/Micro-Manager_File_Formats\">File Formats</a>
  \n
  • <a href=\"/Search_Paths\">Search Paths</a>
  \n
  • <a href=\"/Building_Micro-Manager_Device_Adapters\">Writing Device Adapters</a>
  \n
  • <a href=\"/Free_third-party_tools_for_testing_communications_with_hardware\">Testing communication with hardware</a>
  \n
  • <a href=\"/Building_and_debugging_Micro-Manager_source_code\">Building and Debugging Micro-Manager</a>
  \n
  • <a href=\"/Multi-Dimensional_Acquisition_Programming\">Multi-D Acq. Programming</a>
  \n
  • <a href=\"/Policies_for_inclusion_of_source_code\">Policies for inclusion of source code</a>
  \n
  • <a href=\"https://github.com/micro-manager\">Source code repository history and tickets</a>
  \n
  • APIs

    \n
    • <a href=\"/apidoc/mmstudio/latest/org/micromanager/Studio.html\">2.0 MMStudio API Reference (Java/Beanshell)</a>
    \n
    • <a href=\"/apidoc/mmstudio/1.4/org/micromanager/api/ScriptInterface.html\">1.4 MMStudio API Reference (Java/Beanshell)</a>
    \n
    • <a href=\"/apidoc/mmcorej/latest/mmcorej/CMMCore.html\">Core API Reference (Java/Beanshell)</a>
    \n
    • <a href=\"/apidoc/MMCore/latest/class_c_m_m_core.html\">Core API Reference (C++)</a>
    \n
    • <a href=\"/apidoc/MMDevice/latest/class_m_m_1_1_device.html\">Device API Reference (C++)</a>
    \n

    \n
    \n
  \n\n

  \n
  \n
\n\n\n\n
• <a href=\"/Device_Support\">Devices</a>

  \n
  • <a href=\"/Micro-Manager_Configuration_Guide\">Hardware Configuration Guide</a>
  \n

  \n
  \n
\n\n\n\n
• <a href=\"/Micro-Manager_Community\">Support</a>

  \n
  • <a href=\"/Contact\">Contact</a>
  \n
  • <a href=\"/System_Integrators\">System Integrators</a>
  \n
  • <a href=\"/Programming_Services\">Programming Services</a>
  \n
  • <a href=\"/editing/\">Editing the Wiki</a>

    \n
    • <a href=\"/editing/advanced\">Advanced editing</a>
    \n
    • <a href=\"/editing/buttons\">Buttons</a>
    \n
    • <a href=\"/editing/citations\">Citations</a>
    \n
    • <a class=\"current-page\">Source Code</a>
    \n
    • <a href=\"/editing/headers\">Headers</a>
    \n
    • <a href=\"/editing/icons\">Icons</a>
    \n
    • <a href=\"/editing/images\">Images</a>
    \n
    • <a href=\"/editing/keys\">Keyboard Shortcuts</a>
    \n
    • <a href=\"/editing/linking\">Linking</a>
    \n
    • <a href=\"/editing/math\">Math Expressions</a>
    \n
    • <a href=\"/editing/notices\">Notices</a>
    \n
    • <a href=\"/editing/pitfalls\">Pitfalls</a>
    \n
    • <a href=\"/editing/symbols\">Symbols</a>
    \n
    • <a href=\"/editing/tables\">Tables</a>
    \n
    • <a href=\"/editing/videos\">Videos</a>
    \n
    • <a href=\"/editing/whitespace\">Whitespace</a>
    \n

    \n
    \n
  \n \n

  \n
  \n
\n\n\n\n
• <a href=\"/Credits\">Credits</a>

  \n
  • <a href=\"/Papers_citing_Micro-Manager\">Papers citing MicroManager</a>
  \n
  • <a href=\"/Citing_Micro-Manager\">How to cite MicroManager</a>
  \n

  \n
  \n
\n\n\n

This page describes nice ways of embedding source code in a page.

If you just want to write a short snippet of code as part of a sentence,\nsurround the code in backtick symbols (`).

<code class=\"language-liquid\" data-lang=\"liquid\">Type `print('Hello world!')` and save as `hello.py`.</code>

A “code fence” is three backtick symbols (```) preceding your\ncode, and another three concluding it. Optionally, you can write the name of\nthe language in small case next to the leading fence to declare syntax\nhighlighting is desired with the stated language.

<code class=\"language-liquid\" data-lang=\"liquid\">```java\nImage3DUniverse univ = new Image3DUniverse();\nuniv.show();\nuniv.addMesh(yourImagePlus, null, \"somename\", 50,\n  new boolean[] {true, true, true}, 2);\n```</code>

<code class=\"language-liquid\" data-lang=\"liquid\">```python\ndef update_progress(progress):\n    barLength = 10 # length of progress bar\n    block = int(round(barLength*progress))\n    text = f'\\rPercent complete: ' +\n      f'[{\"#\"*block + \"-\"*(barLength-block)}] ' +\n      f'{progress*100}%'\n    sys.stdout.write(text)\n    sys.stdout.flush()\n```</code>

Alternately, there is a <code class=\"language-plaintext highlighter-rouge\">highlight</code> Liquid directive you can try.\nIt looks like this:

<code class=\"language-liquid\" data-lang=\"liquid\"><span class=\"p\">{%</span><span class=\"w\"> </span><span class=\"nt\">highlight</span><span class=\"w\"> </span>java<span class=\"w\"> </span><span class=\"p\">%}</span>\nlog.info(\"You're a wizard, Harry!\");\nlog.error(\"I'm a what?\");\n<span class=\"p\">{%</span><span class=\"w\"> </span><span class=\"nt\">endhighlight</span><span class=\"w\"> </span><span class=\"p\">%}</span></code>

<code class=\"language-java\" data-lang=\"java\"><span class=\"n\">log</span><span class=\"o\">.</span><span class=\"na\">info</span><span class=\"o\">(</span><span class=\"s\">\"You're a wizard, Harry!\"</span><span class=\"o\">);</span>\n<span class=\"n\">log</span><span class=\"o\">.</span><span class=\"na\">error</span><span class=\"o\">(</span><span class=\"s\">\"I'm a what?\"</span><span class=\"o\">);</span></code>

The <code class=\"language-plaintext highlighter-rouge\">highlight</code> directive and code fences are separate features, but\nfunctionally very similar. If code fences are not working as you like,\ngive the <code class=\"language-plaintext highlighter-rouge\">highlight</code> directive a try to see if it does any better.

If you have a block of code in a GitHub repository, you can embed it\ndynamically into the page using the <code class=\"language-plaintext highlighter-rouge\">github-embed</code> include. This approach has\nthe advantage of avoiding copy-paste skew as the code evolves over time.

<code class=\"language-liquid\" data-lang=\"liquid\"><span class=\"p\">{%</span><span class=\"w\"> </span><span class=\"nt\">include</span><span class=\"w\"> </span><span class=\"nv\">github-embed</span><span class=\"err\">\n</span><span class=\"w\">     </span><span class=\"na\">org</span><span class=\"o\">=</span><span class=\"s2\">\"duckythescientist\"</span><span class=\"err\">\n</span><span class=\"w\">     </span><span class=\"na\">repo</span><span class=\"o\">=</span><span class=\"s2\">\"obfuscatedLife\"</span><span class=\"err\">\n</span><span class=\"w\">     </span><span class=\"na\">branch</span><span class=\"o\">=</span><span class=\"s2\">\"original\"</span><span class=\"err\">\n</span><span class=\"w\">     </span><span class=\"na\">path</span><span class=\"o\">=</span><span class=\"s2\">\"life.c\"</span><span class=\"err\">\n</span><span class=\"w\">     </span><span class=\"na\">label</span><span class=\"o\">=</span><span class=\"s2\">\"Conway's Obfuscated Game of Life\"</span><span class=\"w\"> </span><span class=\"p\">%}</span></code>

Other parameters supported by the <code class=\"language-plaintext highlighter-rouge\">github-embed</code> include are:

* Valid style values are:

This page showcases the look of different header levels.

The best way to collect debugging information is to <a href=\"/editing/advanced\">build the site locally</a>. However if that isn’t an option, this page documents tags which can be helpful.

This page demonstrates how to use the <code class=\"language-plaintext highlighter-rouge\">icon</code> include tag.

`).\n\nUsing headers to delineate content sections has some advantages:\n\n* Headers will automatically have a slugified `id` added,\n to facilitate linking to particular sections using anchors.\n* A table of contents (in the right sidebar by default) will be automatically\n generated according to the declared headers—as long as there are at\n least three of them.\n\n# h1 headers\n\nInvoke header level 1 by writing:\n```markdown\n# Lorem\n```\n\n## h2 headers\n\nInvoke header level 2 by writing:\n```markdown\n## Ipsum\n```\n\n### h3 headers\n\nInvoke header level 3 by writing:\n```markdown\n### Flotsam and Jetsum\n```\n\n#### h4 headers\n\nInvoke header level 4 by writing:\n```markdown\n#### Wingardium Leviosa\n```\n\n##### h5 headers\n\nInvoke header level 5 by writing:\n```markdown\n##### Adamantium\n```\n\n###### h6 headers\n\nInvoke header level 6 by writing:\n```markdown\n###### Plotdevicium\n```\n\n# Closing remarks\n\nThis section here at the bottom exists merely to trigger the table of contents\nto generate on this page, so that you can see how it looks. Cheers!\n", "url": "/editing/headers", "draft": false, "categories": [ ], "title": "Headers", "layout": "page", "section": "Support:Editing the Wiki", "nav-links": true, "slug": "headers", "ext": ".md", "tags": [ ], "date": "2024-12-15 18:00:29 +0000" }, "output": null, "content": "The best way to collect debugging information is to [build the site locally](/editing/advanced). However if that isn't an option, this page documents tags which can be helpful.\n\n## Echo\n\nThis `echo` include just prints its arguments, for debugging/learning purposes. This can be helpful in understanding Liquid syntax and how strings are being read internally by an `include`.\n\nArguments are printed as a comma-separated list of `\"argument\"==>\"value\"` pairs.\n\nNote that liquid allows the passing of [arbitrary arguments](https://jekyllrb.com/docs/includes/) to `include` templates. All these arguments will be stored, but won't have any effect unless the `include`'s [source](https://github.com/micro-manager/micro-manager.github.io/tree/main/_includes) actually does something with those arguments.\n\n{% highlight liquid %}{% raw %}{% include echo content=\"This is the content argument\" bracket=\"what if I pass {}?\" gorilla=\"Why do we have a gorilla argument?\" %}{% endraw %}{% endhighlight %}\n{% include echo content=\"This is the content argument\" bracket=\"what if I pass {}?\" gorilla=\"Why do we have a gorilla argument?\" %}\n\n### What's in a `page`?\n\n{% include notice icon=\"tech\" content=\"Ever wonder what all is part of the `page` data structure? Let's find out!\n\n(You can also do this with the `site` data structure, but be warned: the output will include every page body across the whole site!)\" %}\n\n{% highlight liquid %}{% raw %}{% include echo p=page %}{% endraw %}{% endhighlight %}\n{% include echo p=page %}\n", "url": "/editing/debugging", "draft": false, "categories": [ ], "title": "Debugging", "layout": "page", "section": "Support:Editing the Wiki", "nav-links": true, "slug": "debugging", "ext": ".md", "tags": [ ], "date": "2024-12-15 18:00:29 +0000" }}</p>