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Bio7 2.7 Released


A new version of Bio7 is available. The application Bio7 is an integrated development environment for ecological modeling scientific image analysis and statistical analysis. Over the years Bio7 evolved to a platform useful for a broad scientific context.

This release includes a plethora of new features and improvements for the R editor, RShell, RMarkdown editor and the ImageJ plugin.

Release Notes:


  • Bundled with Java 1.8.52
  • Updated bundled R to version 3.4.3 (Windows)
  • Improved PDF rendering (PDF.js) with Java 1.8.52 (fixed rendering)
  • Updated the Windows SSH client
  • Simplified the dynamic java compilation
  • Updated the Java compiler infrastructure


  • Improved the context information when opening code completion (R-Shell and R editor)
  • Added an improved context information when openening code completion in the R-Shell
  • Context information of a function is shown when using code completion inside function calls
  • Added code completion for function arguments in the R-Shell
  • Added code completion help for ‘library’, ‘require’, ‘data’,’::’ and ‘:::’ functions in the R-Shell and in the R editor

Screencast code completion:

Screencast code completion with particle analysis:

  • Improved code completion for S3 and S4 nested attributes (e.g., x@y$z) also in function calls when cursor is set inside of a composite call
  • Implemented a code completion filter (when typing)
  • Added an option to select different key combinations for the R-Shell code completion (Strg+Space can already be occupied on MacOSX)
  • Added dark theme support for the help browser when opened from the R-Shell help (?)
  • Added a matching brackets selection action to the R-Shell view (Key+Mouse-click before opening or closing bracket)
  • Added an action to transfer the R-Shell history to an opened R editor (see R-Shell help (?))
  • The R-Shell and code completion fonts can now be changed and the size increased
  • The R-Shell is now faster if long text is printed (removed automatic text wrapping)
  • Added the Eclipse Spell Checking infrastructure to the R editor (can be enabled in the preferences)

Screencast spell checking:

  • Spell checking errors can now be fixed in the R editor (hoover action available)
  • Added a preference to enable/disable spell checking
  • Added a ‘Load packages tab’ in the ‘Packages’ view as an UI replacement for the Load packages dialog (improved usability)
  • Added an action to update the display list of installed packages (also triggered if you activate the tab)
  • Added an ‘Attached Packages’ tab to the ‘Packages’ view
  • Added an action to update all packages (‘Load Packages’ tab)

Screencast R Packages view:

  • Improved the R-Shell code completion in general
  • Improved the hoover display layout (for warnings and errors)
  • Fixed several bugs (Reenabled loop parsing and fixed a bug to restore code folding after using code completion in the R editor!)
  • Updated ANTLR parser to version 4.7
  • Added „require“ for package code completion
  • Reduced the memory footprint of the R editor (OS handles)
  • Added missing roxygen tags for code completion of the R editor
  • Created a wizard to support a project template (default folders and files) for reproducible projects
  • Changed key binding of ‘<-‘ and ‘%>%’ operators to make them available in the R-Shell, too (see help in R-Shell)
  • Improved the “Evaluate Selected Line” Action for Rserve (Evaluated when successfully parsed!)

R Markdown editor

  • Spell checking errors in the R markdown editor can now be fixed with a hoover action
  • Added a decent markdown parser (flexmark) to the editor which fixes some minor display problems
  • Added a format action for selected text to the markdown editor

Screencast format markdown selection


  • Updated ImageJ plugin to version 1.51.t16
  • Code completion (template) action now displays the macro documentation when typing
  • Code completion context information improved
  • Images from macros are now opened fast (before had a 2s delay because of a missing ImageJ attribute)
  • Cluttered MACOSX menus are now closed (added from opened application windows and frames). Some default added menus are disabled in the Bio7 preferences by default
  • Macros can now be executed within an external ImageJ instance in a separate Java process (if enabled in the preferences). Windows only!
  • Added Macro debugging context menus to the macro editor

Screencast ImageJ macro debugging:

  • Added an context actions to copy the Macro Recorder code to the current editor
  • Added an „Evaluate Line“ action
  • Reenabled CTRL+X as default „Cut“ text action.

Download and Installation:


Just download the *.zip distribution file from and unzip it in your preferred location. Bio7 comes bundled with a Java Runtime Environment, R and Rserve distribution and works out of the box.


Download and extract the installation file from
For Linux you have to install R and Rserve (see Rserve installation below!).


Download and extract the installation file from

If you start Bio7 a warning or error can occur because of the changes how Apple treats signatures! To allow Bio7 to start see this instructions for Yosemite and Sierra:

OS X Yosemite: Open an app from an unidentified developer

macOS Sierra: Open an app from an unidentified developer

If you have still problems with Sierra see this solution!

In addition For MacOSX you have to install R and Rserve (see below!).

Linux and MacOSX Rserve installation:

To install Rserve open the R shell and then execute the menu action “Options->Install Rserve (coop. mode)”. This will download an install Rserve in your default R library location, see video below (please make sure that your default Linux R library install location has writing permissions!).

The special version of Rserve can also be downloaded here:

For a manual installation in the R prompt type the following command to install the compiled package (replace with your file path!):

install.packages(“Users/yourName/Downloads/Rserve_1.8-4_Mac_cooperative.tgz”, repos=NULL)

Installation of Useful R Packages

R packages which are useful in combination with Bio7 can easily be installed with the main menu “Scripts” action:


Bio7 Documentation

For more information about Bio7 please consult the soon updated Bio7 User Guide.

A plethora of Bio7 videotutorials can be found on YouTube.

ImageJ Plugin with Eclipse Macro Editor Updated


I released a new version of the ImageJ plugin which comes bundled with a feature complete ImageJ macro editor.

For an overview of the plugin please consult the github page:

Release notes:

  • Updated ImageJ plugin to version 1.51.s24
  • Code completion (templates) action now displays the macro documentation when typing
  • Code completion context information improved
  • Images from macros are now opened fast (before had a 2s delay because of a missing attribute)
  • MacOSX extra menu disabled (avoids a cluttered menu)
  • Macros can now be executed within an external ImageJ instance in a separate Java process (if enabled in the preferences – see screenshot 2 below). Tested on Windows only!
  • Added JavaFX library reference for Java9


To install the plugin the latest Eclipse Java version 4.7 (Oxygen) is required (I tested this plugin with 4.7.1a). Open the Help->Install new Software dialog and add the following update site:

The plugin is also availabe from the Eclipse Marketplace Client:

Help->Eclipse Marketplace… (search for ImageJ)

New Icons for Bio7 2.5


Beside many changes for the next release I was able to find the time to update the icons of Bio7 for the next release. The icons are a subset of the FontAwesome icons and some custom icons and were created with Inkscape. They will be made available for free, too.  At the moment the icons are available in two resolutions (100%, 200%) and the larger icons will be used when working with a high DPI monitor (> x dpi). For the rules see:

Here are two screenshots: