20.11.2020

A new version of Bio7 is available. This update comes with a plethora of new features, improvements and bugfixes.

Bio7 3.2 Dark theme enabled using the spatstat package examples and plots.

For those who don’t know Bio7. The application Bio7 is an integrated development environment for ecological modeling, scientific image analysis and statistical analysis.

It also contains a feature complete development environment for R with an advanced R editor, R developer tools and interfaces to perform scientific image analysis with R and the embedded ImageJ application.

New and Noteworthy

General:

• Bio7 3.2 RCP (Rich Client Platform) built upon Eclipse 4.17
• Bundled with AdoptOpenJDK 14.0.2 and JavaFX 15
• Bundled with R 4.0.3 (Windows only!)
• Added an image classification plugin for supervised and unsupervised image classification (using R and ImageJ – see R-Shell view context menu “Image Classification”). For an overview and details, see: https://github.com/Bio7/Bio7_Classification

Image Classification plugin (Dark Theme enabled)

• Menus and scrollbars are now dark on Windows, too
• Improved the dynamic script menus. Nested folders can be hidden for complex Java plugins (see image classification plugin).
• Updated several Java libraries (Groovy, POI, etc.)
• Improved several view layouts (showing scrollbars if necessary)
• Changed all SWT ExpandBars to CTabFolders to improve the display when the dark theme is selected
• Added more default fast wizards actions to the toolbar menu (to create Bio7 projects with files in one action)

Opened fast wizard menu (Dark Theme enabled)

• Added new API methods (e.g., an R script job interface)
• Enabled the recognition of Eclipse supported ASCII control characters in the console (see preferences)
• Improved the compilation of pure LaTeX files without the necessity to run Rserve
• Improved the dark theme on Windows, Linux and MacOSX

ImageJ

• Updated the ImageJ plugin to version 1.53g34 (see ImageJ release notes)
• Improved the visual interface for debugging
• The main view menu can now be extended dynamically from plugins
• ImageJ macros updated
• Toolbar menus improved
• Converted the ImageJ toolbar menus to SWT to display the dark theme
• Converted several ImageJ context menus to SWT (recognizable on HighDPI, Linux GTK)
• For all changes since the last release, see: https://github.com/Bio7/EclipseImageJ1Plugin

R

• Updated the embedded R application on Windows
• The R plugin can now be updated individually
• Added a new ‘Load Packages’ table to display installed R packages and if updates available (selected packages can be updated in this view, too)

Load Packages tab (Dark Theme)

• Added a grammar rule for raw string literals to the R editor (thanks to Bart Kiers)
• Added a database preference to store the XML database profile file in a different (secret) location.
• Fixed some minor R-Shell bugs

R + ImageJ

• Added an option to transfer ImageJ ROI groups or special ROI names as class signatures to R (ROI Manager transfer actions in the Image-Methods view)
• Improved the ROI stack transfer for virtual stacks (to load and transfer disk resident image stacks)
• Improved several functions for the new image classification plugin

Download and Installation:

Windows:

Just download the *.zip distribution file from https://bio7.org 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.

Linux:

Download and extract the installation file from https://bio7.org.
For Linux you have to install R and Rserve (see Rserve installation below!).

MacOSX:

Download and extract the installation file from https://bio7.org.

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, Sierra, Mojave and Big Sur:

First try to open the app with the context menu to allow the execution. If that won’t work try the following:

Yosemite: Open an app from an unidentified developer

Sierra: Open an app from an unidentified developer

Moave and Sierra: How to fix “Application” is damaged and can’t be opened error in macOS Mojave and High Sierra.

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

Linux and MacOSX Rserve (compiled for cooperative mode) installation:

To install Rserve open the ‘Native R’ console in the ‘Console’ view and then execute the view menu action “Options -> Install Rserve (coop. mode) for R …” for different R versions (SSL 1.1 version for Linux Ubuntu > 19.10).
This will download and 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!):

How to install Rserve for Linux and MacOSX: https://youtu.be/tF7HbRBRIF

In cooperative mode only one connection at a time is allowed (which we want for this Desktop apl.) and all subsequent connections share the same namespace (default on Windows)!

Bio7 Documentation

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

A plethora of Bio7 videotutorials for an introduction can be found on YouTube.