Landscape Metrics with R, SDMTools, ImageJ and Bio7

February 2, 2012
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(This article was first published on » R, and kindly contributed to R-bloggers)

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 data) with landscape metrics. A typical workflow would include to cluster available image data into different classes and then analyze the data with the available metrics.

In the video below a simple artificial example is given of the workflow in Bio7 with the help of ImageJ, R and the “SDMTools” package:

http://bio7.org/flash/landscape.htm

Beside this possibility it is also possible to calculate a subset of landscape metrics with a Java API available in Bio7 for simulation purposes.

Apropos:

Landscape metrics algorithms are quite similar to some algorithms which are default available in ImageJ and these measurements can maybe complement an analysis of landscape structures, see:

http://rsbweb.nih.gov/ij/docs/menus/analyze.html
http://bio7.org/flash/clusterParticles.htm

Be aware that it is of importance to define the neighborhood rule (e.g. 4- neighbor rule or 8-neighbor rule) beside several other aspects which have to be considered. For an overview about landscape analysis and landscape ecology follow the link to a literature database at the end of this post.

Related to this article:

Creating fractal categorical maps and images with Bio7
http://www.uni-bielefeld.de/biologie/Oekosystembiologie/bio7app/flashtut/fractalrandom.htm

Supervised classification of images with Bio7 and R
http://www.uni-bielefeld.de/biologie/Oekosystembiologie/bio7app/flashtut/supervisedimages.htm

SDMTools package
http://cran.r-project.org/web/packages/SDMTools/index.html

Literature (see Landscape Analysis – if you know good papers or books let me know!)
https://www.zotero.org/groups/ecological_modelling/items

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