18.05.2015

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:

http://bio7.org

Release notes Bio7 2.1:

R:

• 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.

ImageJ

• 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.

WorldWind

• 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.

3D

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

Python

• 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.

Java

• 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.

Examples:

• Added and fixed some examples for Bio7

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.exe file.

For more information about Bio7:

Documentation

YouTube Videos