Articles by » R

Bio7 2.0 for Linux Released!

January 31, 2015 | » R

01.02.2015 I released the Linux version of Bio7 2.0 (see screenshot below). For an overview of the new Bio7 features follow the link: Bio7 2.0 new features Added Linux features: A new Java menu action (in the Scripts menu) is available to start a Py4J server which can communicate to Java and ... [Read more...]

Image Data Transfer to R with ImageJ and Bio7 2.0

December 9, 2014 | » R

09.12.2014 In the new version of Bio7 2.0 i added some new easy to use functions to transfer image data from ImageJ to R. For example, you can now drag a folder of images on the ImageJ-Canvas view, open them memory efficient as a virtual stack in ImageJ and transfer them with ... [Read more...]

Bio7 2.0 for Windows Released!

December 1, 2014 | » R

01.12.2014 A new Windows version of Bio7 is available. Many new features have been added to Bio7 2.0 which is now based on Eclipse 4.4. Highlights are the improved R editor, the R debugging Graphical User Interface (using the standard R debugger), the integrated Java Development Tools (JDT) to create Java simulation models ... [Read more...]

R Debugging GUI Improvements for Bio7

November 20, 2014 | » R

20.11.2014 In my last post i presented the first version of a debugging GUI for R in Bio7 which is just a visual wrapper for the default R debugging functions. In the meantime i added some new methods and also improved the visualization. For the upcoming Bio7 release i have to ... [Read more...]

Simple R Debugging GUI for Bio7

September 26, 2014 | » R

26.09.2014 For the next release of Bio7 I implemented a first simple debugging GUI (Graphical User Interface) for R scripts. For the debugging process a change from Rserve to an available Java R console connection in Bio7 is necessary (with Rserve alone a debugging interface wouldn’t be possible). Both connections ... [Read more...]

Bio7 R Documentation and Plot Examples

July 18, 2014 | » R

18.07.2014 A very time expensive process is the documentation of software you created yourself. I was finally able to update and improve the documentation for Bio7 and the embedded R “Graphical User Interface”. For the documentation this time i used Lyx to export the LaTeX document as HTML with the available ... [Read more...]

R editor improvements for Bio7

January 31, 2014 | » R

30.01.2014 For the next release of Bio7 based on Eclipse 4.4 an improvement of the R editor for a much better editing experience of R scripts will be available. The integrated editor itself is built bottom-up (based upon an Eclipse editor editor template) although there a great editor frameworks (DLTK) or frameworks ... [Read more...]

Bio7 1.7.1 MacOSX Released

October 15, 2013 | » R

15.10.2013 Finally i released  Bio7 1.7.1 for MacOSX. This release is bundled with a Java Runtime Environment and the latest R version (3.0.2) for MacOSX. For the plot functionality eventually XQuartz has to be installed (if not already installed!). Please note the installation requirements at the bottom of the page. Here are some ... [Read more...]

Bio7 1.7.1 for Linux Released

September 24, 2013 | » R

24.09.2013 I released a new Linux version of Bio7 (64-bit only – see Screenshots below). For an overview of the new features please read the release notes for Windows 1.7.0 and 1.7.1: In addition some Linux specific improvements are embedded in this release. Additional Linux features: ... [Read more...]

New Bio7 1.7.1 Release with Improved R Plot Image Display

September 6, 2013 | » R

05.09.2013 I released a new Windows version of Bio7. This release improves the general R plot functionality of Bio7. The default image plots are now displayed in a Image stack if more than one plot command is executed. In this way all plots are automatically openend and not only the last ... [Read more...]

Bio7 1.7 for Windows Released!

August 8, 2013 | » R

07.08.2013 A new Windows version of Bio7 is available. This version comes with a lot of new features and improvements for Java, R and ImageJ. One highlight is that you can now interpret Jython (Python) code with Bio7. In addition a new console implementation is available which offers access to a ... [Read more...]

Cluster Multiple Images with ImageJ and R

August 31, 2012 | » R

30.08.2012 With Bio7 1.6 it is possible to send multiple images from ImageJ to R without the need to open them in the Graphical User Interface of ImageJ for speed improvements. With a simple script written in Java, Groovy or BeanShell a new Bio7 API command can be used (see below) to ... [Read more...]

Bio7 1.6 for Windows and Linux released!

August 1, 2012 | » R

01.08.2012 Finally i released a new version of Bio7 with many improvements and new features. Updated tutorials are available, too. The new Bio7 1.6 release can be downloaded here. Please also download the examples *.zip file from the sourceforge website which contains new examples for Bio7 1.6 (e.g. an example to cluster ... [Read more...]

Landscape Metrics with R, SDMTools, ImageJ and Bio7

February 2, 2012 | » R

01.02.2012 Landscape metrics were developed to analyze spatial patterns of landscapes (e.g. composition and spatial arrangement). In R it is possible to calculate these metrics with the “SDMTools” package. Bio7 offers an easy to use interface to R and ImageJ and can use these tools to simplify a workflow to ... [Read more...]

Image Data from ImageJ to R and Vice Versa

August 5, 2011 | » R

In recent years many R packages have been developed to enable image analysis in R. As an alternative the combination of R with a powerful image analysis software like ImageJ offers many advanced image analysis interfaces and algorithms not yet available in R. Bio7 integrates both applications in a Rich ... [Read more...]

Shared Ecological Modelling References

June 6, 2011 | » R

05.06.2011 Today i started to create a list of books and articles about ecological modelling. In this list you will not only find general books about modelling but also books about spatial analysis, image analysis and other (in my opinion) important techniques useful in the context of ecological modelling. For the ... [Read more...]

Image Classification Limits Part 2

March 31, 2011 | » R

Recently i released the first 64-bit versions of Bio7 bundled with a 64-bit Java Virtual Machine. I’m always curious how far i can go using both applications together to do image analysis (especially classification) with huge images coming e.g. from satellites. The transfer of the images in Bio7 ... [Read more...]

New R features in Bio7 1.5

February 20, 2011 | » R

Bio7 1.5 has been released and comes with new functionalities for R. For all who don’t know Bio7 here is a short description: Bio7 is a integrated development environment for ecological modelling based on the Rich-Client-Platform concept of the Java IDE Eclipse. The Bio7 platform contains several perspectives which arrange ... [Read more...]

Image Data and Classification with R

August 3, 2010 | » R

03.08.2010 In this post i would like to demonstrate the ability of R to handle and classify image data with the help of ImageJ and Rserve bundled and implemented in Bio7. In general R is a very useful application for image analysis and plenty of “pure” R packages for image analysis ... [Read more...]

Plots in R and the ImageJ visualization

April 1, 2010 | » R

If you plot data in R and you would like to display the same data in the ImageJ view it is necessary to transfer the data matrix to ImageJ. The first thing which can be noticed is that the image data is displayed rotated because of the Bio7 approach to ... [Read more...]
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