Blog Archives

Cluster Multiple Images with ImageJ and R

August 31, 2012
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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 transfer images and

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Bio7 1.6 for Windows and Linux released!

August 1, 2012
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Bio7 1.6 for Windows and Linux released!

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 an image folder with

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Landscape Metrics with R, SDMTools, ImageJ and Bio7

February 2, 2012
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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 analyze image data (e.g. vegetation

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Image Data from ImageJ to R and Vice Versa

August 5, 2011
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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 Client Plattform based on Eclipse

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Shared Ecological Modelling References

June 6, 2011
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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 collection i use “Zotero”

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Image Classification Limits Part 2

March 31, 2011
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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 is realized with a combination of ImageJ

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New R features in Bio7 1.5

February 20, 2011
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New R features in Bio7 1.5

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 several views for a special

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Image Data and Classification with R

August 3, 2010
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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 are already available. But

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Plots in R and the ImageJ visualization

April 1, 2010
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Plots in R and the ImageJ visualization

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 transfer data forth and back

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Ecological Modelling with “R”

March 7, 2010
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Here i present some Books and Articles about Ecological Modelling and “R”. Since “R” is integrated in Bio7 all the presented methods in the Books and Articles can also be useful together with Bio7. Books: Ellner, Stephen P. & Guckenheimer, John (2006). Dynamic Models in Biology. Princeton University Press Bolker B (2008) Ecological Models and

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