Bio7 at the useR! Conference 2015

I recently released a new version of Bio7 just in time and planned for the useR conference 2015 where I will present Bio7 in the Ecology oral session titled:

“A Graphical User Interface for R in an Integrated Development Environment for Ecological Modeling, Scientific Image Analysis and Statistical Analysis “.

I hope to see you there and if you have any questions about Bio7 don’t hesitate to contact me. I’m looking forward to the conference.

Bio7 2.2 for Windows, Linux and MacOSX released


I released a new version of Bio7 for Windows, Linux and MacOSX simultaneously. This release is based on Eclipse 4.5 which was published on Wednesday.
It comes bundled with the latest ImageJ version (1.49u) and the latest R version (bundled with Windows and Mac).

Download at:

New features:

  • Based on Eclipse 4.5 (Mars)
  • Updated ImageJ to 1.49u
  • Updated R to version 3.2.1
  • HTML editor has now an enabled “Outline” view (with the help of a HTML parser)
  • New feature and action (main toolbar) to create knitr HTML reports easily  (just add R commands in a HTML div layer which can be created with the knitr action in the GUI HTML editor toolbar – see screenshot below)


  • Added default knitr HTML preferences
  • Added more R editor preferences
  • Improved the MacOSX GUI
  • Updated all scientific libraries for Java (Commons Math, etc.)
  • Improved the dynamic invocation of the Java main method (now an empty string is passed)
  • Updated the Groovy interpreter


Simply unzip the archive of Bio7 2.2 (Windows, Linux) in your preferred OS location. The Mac version can be installed easily with the available *.dmg file installer.

Linux only: R and Rserve have to be installed. Please install Rserve in cooperative mode for Bio7: sudo PKG_CPPFLAGS=-DCOOPERATIVE R CMD INSTALL Rserve_1.8-1.tar.gz

See: Bio7 documentation









Bio7 2.1 Release Candidate RC2 for MacOSX Available


I published a MacOSX release candidate for Bio7 2.1 based on Eclipse 4.5 RC2. This release was tested on MacOSX 10.10. The final release will be published after the official Eclipse 4.5 release.



  • Bio7 2.1 comes as a regular *.dmg installation package. Just drag the to the Applications folder.
  • Bio7 2.1 comes with a bundled jre 1.8.45. No need to install an extra Java Runtime Environment.
  • Bio7 2.1 comes bundled with R 3.2.0 and Rserve 1.8.2 installed.

Eventually XQuartz has to be installed to use the default custom R plotting device of Bio7 on MacOSX. If you plot the first time with R and XQuartz is not available a dialog will inform about the missing package.

Download Bio7 at:

Bio7 2.1 for Linux 64-bit and Windows 32-bit released


After the 64-bit release of Windows the Linux 64-bit and Windows 32-bit release can be downloaded at:


Linux installation:

The installation of Bio7 is similar to the installation of the Eclipse environment. Simply decompress the downloaded *.zip file in a preferred location on your file system. After decompressing with a standard zip-tool (like WinZip, Win Rar) the typical file structure of an Eclipse based application will be created. To start the application simply double click on the  Bio7 binary file.

R  and Rserve installation:

To use R from within Bio7 please install R with a Linux R package manager.
Also the installation of the Rserve library is required. Rserve hast be compiled and installed in the local R application with the shell command:


The flag before R CMD INSTALL… is necessary to enable a shared workspace when switching from a local Rserve connection to the native Bio7 R console and conversely. After the installation of R the path to the R (if not using the default path!) application has to be adjusted inside of Bio7 (Preferences- ▷ Preferences Bio7). In addition the path to the (add-on) packages install location has to be adjusted, too (Preferences ▷ Preferences Bio7 ▷ RServe Preferences).
Please also set the user rights for the folder. This is sometimes necessary if you would like to install packages with the Bio7 interface and you don’t have the user rights.
Since Bio7 1.4 default R paths are set which are usually correct for a Linux distribution!


Bio7 2.1 for Windows 64 bit released


I released a new version of the Integrated Development Environment Bio7 with new functions and many visual layout improvements of the Bio7 Graphical User Interface.

Bio7 2.1 can be downloaded here:

Release notes Bio7 2.1:


  • Updated R to version 3.2.0.
  • Improved the R perspective layout (see below).


  • Improved the syntax coloring and grammar (assignment, multiline string, infix operator for package ‘data.table’)
  • Improved the layout of the R-Shell view for higher dpi’s
  • Added code folding for ‘if’,’while’, ‘repeat’ and ‘for’ expressions.
  • Added options to enable or disable codefolding, code context (mark words, info popup) and code completion.
  • The line numbering of the R editor is now enabled by default.
  • Improved the “Install package(s)” GUI and other dialogs.


  • Updated ImageJ to 1.49t
  • Added Bio7 ImageJ preferences for special dialogs to stay on top (ROI Manager, Results Table, Macro Recorder).
  • Added extra action panels for the histogram and profile plot to enable the new ImageJ actions.

  • Resized the layout of the ‘ImageJ-Toolbar’ and ‘Image-Methods’ view.
  • Improved the compatibility for the 3D viewer plugin and the OMERO (The Open Microscopy Environment) client.
  • Added options to resize and store the dimensions of the ‘Image-Methods’ dialog and the ‘ImageJ-Toolbar’ in the preferences.
  • Added more tooltips for context information.


  • Improved the layout for the different actions and layers.
  • Added an option to load a GEOTIFF image data parallel in ImageJ when added as a layer to WorldWind.
  • Added an easier to use alpha value function for transparent image regions (from ImageJ – see below).

  • Greyscale and float images can now be displayed as RGBA if enabled (tranparent regions).
  • Added a ‘Location’ action for loaded shapefiles.
  • Improved the GDAL loading. Now GDAL (Java) can be called from within Bio7 dynamically.


  • Improved the layout and actions for the different 3D panels.


  • Added Py4J library for the communication between Java and Cpython.
  • Added a server start/stop action for Py4J available in the Scripts menu.
  • Added a Py4J example (ImageJ measurement) in the Bio7 documentation.
  • As an alternative you can now install the Eclipse Python editor PyDev and execute the python script within the Bio7 connection or in the PyDev editor process.
  • Added support to eval Python3.x scripts (can be enabled in the preferences).

Bio7 GUI

  • Improved the startup layout for Bio7. The application now starts maximized.
  • Increased the Bio7 splashscreen.


  • Updated the embedded Java Runtime Environment to 1.8.45.
  • Updated the integrated JavaFX SceneBuilderKit.


  • Added support for Java3D built on JOGL.
  • Added a default ‘close’ action in the base (abstract) Model class.
  • The ‘close’ method is called automatically if a custom view is closed.


  • Added and fixed some examples for Bio7


The installation of Bio7 is similar to the installation of the Eclipse environment. Simply decompress the downloaded *.zip file in a preferred location on your file system. After decompressing with a standard zip-tool (like WinZip, Win Rar) the typical file structure of an Eclipse based application will be created. To start the application simply double click on the Bio7.exe file.

For more information about Bio7:


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