Bio7 2.4 for Windows and Mac Released

A new release of Bio7 is available for Windows and MacOSX. The Linux version will be released soon, too. This release comes with a plethora of new functions, especially for the R editor.

Download at:

Release notes:


  • Updated Bio7 to use Eclipse 4.6 (Neon) as RCP basis
  • Updated the embedded Java Runtime Environment to version 1.8.92
  • Updated embedded R for Windows to R 3.3.1
  • Improved the toolbar layout and action alignments (CSS can be edited!)
  • Added a new ImageJ R analysis perspective


  • Added a new R debug perspective
  • Added a new and easy to use text preference field to execute Groovy script commands at startup (beside any scripts in the startup folder!) to open, e.g., a custom perspective, or startup R  if enabled.


  • The Quadgrid, Linechart, Piechart and the Points view are now embedded in a Swt JavaFX panel and can be fullscreened (F1, F2, F3, F4, F5 – F1 key is Windows only!)
  • Added a terminate (Java controlled) and kill R process (OS controlled) action to the main toolbar of Bio7.


  • At R/Rserve startup a new check for a running R instance is executed with an option to kill all running R instances (to avoid a wrong connection to a running instance from an crashed Bio7 R session).
  • Added  many new Bio7 R command key shortcuts
  • Added an install R packages script to install some useful default R packages for Bio7

R editor:

  • The R editor has been transferred to it’s own Github repository and can be updated as a plugin
  • Improved and formatted the display of the error messages
  • Improved massively the speed for parsing and marker creation
  • Added many new R editor key shortcuts to speed up editing
  • Added an action to the context menu to open the plot preferences
  • Added an action to the context menu to open the font preferences
  • Added a RServe formatR action to the context menu
  • Added a Profile script action for the profvis package to the context menu
  • Added a Profile script selection action for the profvis package to the context menu
  • Added a color dialog to the context menu. A selected R,G,B color will be displayed and set in the editor
  • Added an “Reload Package Completion” action to the context menu to load completion help for loaded packages (decrease warnings by known methods, increase available code completion templates – The same action is available in the R-Shell view evaluation textfield).


  • The Load/Remove packages(s) dialog has a new action to transfer available selected package names to the R editor (as ‘library(package)’)
  • Now warnings and errors are displayed more consistently. If a quick fix is available it will be indicated with a warning/error quick fix icon instead of a default warning/error icon
  • Added new quick fixes to the R editor
  • Quick fixes and warning messages can now be displayed and fixed by hoovering over the underlined editor marker
  • Added the automatic close of {braces}, (parentheses), [brackets], “strings” and ‘strings’. It can be disabled in the preferences
  • Improved the speed of the ‘Mark selected word’ action (scope independant) which can be enabled in the preferences

R editor refactoring

  • Added an ‘Extract Method’ action which parses and extract a method from a selected text if valid


  • Added an ‘Extract Variable’ action which parses and extracts a variable from a selected text if valid
  • Added a ‘Create new File from Clipboard’ action which parses and creates a new file from the clipboard text if valid in the project folder and opens the R file for editing
  • Added an ‘Extract Editor Selection to File’ action which parses and creates a new file from a selection if valid in the project folder and opens the R file for editing

R editor code analysis:

  • Added an analysis function to detect Unused Functions
  • Added an analysis function to detect if a function is available
  • Added an analysis function to detect if a variable is used
  • Added an analysis function to detect if a variable is available
  • Added an analysis function to check for wrong constants (na, true, false, null)
  • Added an analysis function to check for functions if a function (or variable) with that name is already defined
  • Added an analysis function to check for variables if a variable (or function) with that name is already defined
  • Added an analysis function to check if a function call argument is missing
  • Added an analysis function to check if a function call has to many arguments
  • Added an analysis function to check if the name of a variable assignment in a function call is wrong
  • Added an analysis function to check a function call with parameter on a parameterless function
  • Added an analysis function to check variables in function calls and square brackets
  • Added options in the preferences to enable/disable the code analysis functions


R Outline View

  • Added the display of loop variables to the outline view
  • Added the display of function call variable assignments to the outline view
  • Added the display of S3,S4, References and R6 classes to the outline view (S3 classes are only detected with class(x), References classes and R6 classes functions are not displayed nested!)


R editor code completion

  • The sorting of the code completion dialog has been improved
  • The code completion dialog now displays local defined variables and methods available in the current scope
  • Added a new function in the code completion popup dialog to open the template preferences faster


  • If the code completion is opened in a method call the arguments of the function will be displayed in a new table dialog. However if an function or variable is started within the method call the regular code completion is shown (for nested functions or variables call)


  • Added two actions in the hoover help dialog to open the help browser (?) or search in the Rdocumentation website


  • The code completion dialog can now be configured in the preferences to open automatically on key typing  (number of typed chars and chars can be configured, too).

R-Shell view

  • The R text is now validated with the Bio7 default R code parser
  • Added an error marker to the textfield if a parsing error occurs
  • Added code completions to the evaluate expression textfield (Ctrl+Space). Code completion is only available in nested calls after open parentheses


  • A help file browser can now be opened from selected text (e.g., nested function).
  • Native connection commands can now be executed in the evaluate expression textfield

R Markdown

  • Now JavaScript is enabled for the HTML-Browser by default
  • Added a new option to scale the JavaFX browser content if enabled  (handy for R markdown presentations). The JavaFX  browser can be fullscreened (F1,F2,F3 – secondary monitor…..)

Table view

  • Improved massively the speed of the close operation of a table sheet
  • Improved the CSV importer with more options to import data with a dynamic preview
  • The CSV importer now accepts clipboard data if selected
  • The preview table is now updated dynamically if changes occur



  • Updated ImageJ to version 1.51d
  • Added a subset of ImageJ2 libraries in a new ImageJ2 Eclipse plugin
  • Improved the ROI image pixel data transfer methods. Now selected ROI’s pixels are transferred. If no selection is available all ROI‘s will be transferred!
  • The ROI transfer methods now also accept points and lines (please note that line pixels are interpolated in the ImageJ results table by default)
  • The Bio7 ImageJ plugin can now be updated or installed individually
  • ImageJ panels can now be opened in a JavaFX panel embedded in SWT (experimental) if enabled in the preferences


  • Updated all Java libraries
  • Update the JavaFX SceneBuilder to version 2.2
  • The JavaFX SceneBuilder controller class created variables and methods are now ‘public’ by default.
  • Added support for LibreOffice 5. Now the Bio7 LibreOffice functions work again with LibreOffice 5.

Eclipse Neon features



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


Just download and execute the *.dmg installation file from

To use R and Rserve you have to install R for MacOSX.

In addition you have to install Rserve configured to use ‘cooperative mode’ (shared workspace in Rserve and R mode) which can be downloaded here:

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)

You can also compile Rserve by yourself. For an HowTo please consult the Bio7 documentation here.


Added a tiny script to install useful default R packages for Bio7 to use all available GUI functionalities (e.g. rmarkdown, rgdal, spatstat, formatR, knitr, etc.). To install the scripts start Rserve and execute the action Scripts->RScripts->Install_R_Packages.

The script will install the R packages.

For MacOSX it could be that you have to select a mirror in the Bio7 Console (shell). Type in a number (1- …) and press return to start the installation if no shell message is displayed. The R installation script can be edited in /plugins/ Suggestions for improvements are welcome.



R editor improvements for the next release of Bio7


For the upcoming release of Bio7 I worked hard to improve the R editor features. So I added some new features and improvements to assist in the creation of R scripts in Bio7.
One of the highlights is the newly integrated dynamic code analysis when writing an R script.

Here a short overview of some new R editor features I integrated so far:

  • Detect and display unused variables and functions


  • Detect missing functions and variables
  • Added a new code assist list when triggered in function calls


  • Check of function arguments


  • Check of wrong function argument


  • Available help for mistyped functions (% similarity)


  • Improved Code Completion in general
  • Added a toolbar with two HTML help actions to the context help dialog (if you hover over a method)


  • Improved Code Completion to list local scope self defined variables and functions


  • Added  an refactor action to extract variables
  • Added an refactor action to extract functions


  • Added more Quickfixes
  • Quickfixes can now be opened by hovering over a problem or error marker
  • Added an automatic close action of parentheses, brackets, braces and strings in the editor
  • Improved the general parsing speed
  • Added new key shortcuts to faster perform R editor actions
  • New action and key shortcut to open the plot preferences faster
  • Added new on/off preferences for the new features
  • Improved the display of the Outline view for variables and functions

There is of course some room for improvements and there are some rough edges in the implementation of the dynamic code analysis since the R language is a highly dynamic language. However I hope that this features will be a help in the creation of correct R scripts in the R editor of the next Bio7 release.

Useful Eclipse Plugins for Bio7


Here are some great Eclipse plugins useful in a scientific context which can be installed directly into Bio7 with the Eclipse Update-Manager of Bio7 (Help->Install New Software…).

Please note that you can also install the Eclipse Marketplace Client into Bio7 to install some of these plugins (a fancy interface to search for plugins):

The powerful Git plugin to connect Bio7 with a Git repository.

A true native terminal with SSH,Telnet and Serial line support.

Eclipse CDT
C/C++ editor and development tooling.

Arduino C++ IDE:
A great Arduino extension of the C++ editor of Eclipse.

An integrated development environment to support the development of parallel applications written in C, C++, and Fortran.

An Integrated Development Environment and Refactoring Tool for Fortran

JavaScript editor and development tools

PyDev Editor:
A very powerful Python editor which can be used to execute Bio7 Jython and Python scripts instead of the Bio7 default editor. In addition Bio7 can use the PyDev editor to execute scripts running on the Bio7 Java classpath. If you open Jython/Python scripts with the PyDev editor the default Bio7 action will be visible to execute the scripts on the Bio7 classpath.

Groovy Editor:
A more powerful Groovy editor. Can also be used with the Bio7 classpath if scripts are opened with this editor instead of the default.

Jeeeyul’s Eclipse Themes
To install new styling themes into Bio7.

Eclipse Color Theme
If you need, e.g., a dark colored editor at night to rest your eyes.

Julia Editor
A Julia editor in an early stage. But very promising.

Remote System Explorer
A plugin to connect Bio7 with SSH, Telnet, FTP and DStore protocols.

This is a selection of a huge amount of available Eclipse plugins which can be installed into Bio7 to complement the default tools.

Supervised Image Classification With Bio7, R And ImageJ


I created a new Bio7 example which demonstrates how to classify an image with Bio7, ImageJ and R.


For the classification I used the “randomForest” R package and an image example of ImageJ so you can reproduce the example quite easily. I made the example script as easy as possible and trained the classifier with 64 trees by default (see literature below). Not shown in the video is the procedure to control the prediction of the trained classifier with test data. You can find a simple script in the repository, too, which uses a method of the powerful ‘caret’ package.


If you have some recommendations of how to effectively use a decent classifier for image classification (e.g., which classifier is well suited for images, which tuning parameters are useful in this context, which additional signatures could be used, etc.) I would be happy to hear.


Fernández-Delgado, M., Cernadas, E., Barro, S. & Amorim, D. Do we Need Hundreds of Classifiers to Solve Real World Classification Problems? Journal of Machine Learning Research 15, 3133–3181 (2014).

Oshiro, T. M., Perez, P. S. & Baranauskas, J. A. in Machine Learning and Data Mining in Pattern Recognition (ed. Perner, P.) 154–168 (Springer Berlin Heidelberg, 2012).

Latinne, P., Latinne, P., Debeir, O. & Decaestecker, C. Limiting the Number of Trees in Random Forests. IN PROCEEDINGS OF MCS 2001, LNCS 2096, 2001.