Bio7 2.1 for Windows 64 bit released

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).

rper

  • 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.

scenebuilder

  • 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

Knitr with Bio7

16.04.2015

In Bio7 it is possible to write a documentation in knitr. A simple visual and textual HTML editor (based on JavaFX) and an embedded Latex editor (based on TeXclipse) helps in the creation of a *.html or *.pdf documentation. For the *.pdf creation a TeX environment has to be available (Windows e.g. MiKTeX).

Overview video:

Note that there is still a bug in the visual JavaFX HTML editor (JavaFX SWT bug) to select text in the visual part of the editor. A workaround is to use the combination of Shift- or Ctrl-key and a mouse-click.

In upcoming releases more improvements for R reports will be available in Bio7.

 

Bio7 2.0 for Windows 32 bit Release

24.03.2015

Because of some requests of a Windows 32 bit version of Bio7 2.0 I uploaded a built to sourceforge.

Release notes:

  • Updated R to version 3.1.3
  • Updated ImageJ to version 1.49p
  • Added some ImageJ dialog options (to stay on top, e.g., the ROI Manager)
  • Updated Java to version 1.8.40
  • Updated the JavaFX embedded SceneBuilder to Java 1.8.40

If you don’t know Bio7 here is an overview of the features (not only R):

Bio7 can be downloaded here:

http://bio7.org

Documentation and Videos Tutorials:

Documentation

Video Tutorials YouTube

 

 

Solving CentOS 7, Fedora Problems at Startup Wrong Layouts

02.02.2015

Here I describe some notable Linux distribution errors which can be corrected with the following startup options (1) and CSS changes (2).

1. Startup Problems

There seems to be problems with CentOS 7  in general. If the application does not start correctly, e.g., the Bio7 window will not be shown then add the following arg (e.g., with a text editor) to the Bio7.ini file in the Bio7 base folder (installation folder).

–launcher.GTK_version
2

This arg had to be added like this in the*.ini file (see screenshot – don’t place it wrong else an error will occur!):

centosarg

After saving the file Bio7 should be started on CentOS 7 (see screenshot below)! Please note that you can also adjust the Java memory there.

centos7

Another rare error occuring in Fedora is described here!.
However I tested Bio7 on the latest Fedora release and Bio7 started without any problems.

2. Layout Problems

If the layout of your distribution seems to be distorted (e.g., maximize buttons are to small – could be occuring in the default layout of Fedora and CentOS!) this can be corrected in the Bio7 CSS. The file can be found under:

/yourBio7folder/plugins/com.eco.bio7.themes_2.0.0.201412011620/css/e4_default_win7.css
(win7.css was reused for Linux so please don’t wonder)

The following changed css attributes will correct the height of the toolbars (changed attributes in bold):

.MPartStack {
……………………………………
color: ‘#org-eclipse-ui-workbench-INACTIVE_TAB_TEXT_COLOR';
 swt-tab-height: 36.0px;

}

.MPartStack.active {
…………………………………..
swt-shadow-visible: false;
 swt-tab-height: 36.0px;
}

/*Important to set height for the view menus!*/
CTabFolder {
swt-corner-radius: 15.0;
swt-tab-height: 36.0px;
}

Of course you can change other attributes as well, e.g.,  if you want to change a color.