ROXAS

Downloads

ROXAS 1.3 Basic (4.96 MB)

ROXAS 1.4 Pro (register to get download link)

Examples

1 - Example of ROXAS analysis with Quercus petraea tree core sample, before (left) and after (right) automatic analysis. Cutout image of scanned surface, original resolution: 0.06 pixels/µm, original image dimensions: 500 x 4000 pixels. Photo credit: P. Fonti

2 - Example of ROXAS analysis with Populus sp. tree core sample, before (left) and after (right) automatic analysis. Cutout image of thin section (30 µm), original resolution: 0.23 pixels/µm, original image dimensions: 900 x 11.500 pixels.

3 - Example of ROXAS analysis with Sanguisorba minor root cross-section (30 µm), before (left) and after (right) analysis. Image of thin section, original resolution: 0.63 pixels/µm, original image dimensions: 1500 x 1000 pixels

ROXAS is a tool for the quantitative analysis of xylem anatomy in cross-sections and cores of trees (angiosperms and conifers), shrubs and herbaceous plants. 

Varying levels of automation ranging from automatic batch processing to fully manual analysis mode – or a combination of both that includes, for instance, manual editing of aberrant ring borders or eliminating wrong vessels – give the user the desired level of control. Adjusting a wide range of ROXAS settings parameters help to optimize recognition scores of automatic analysis. Yet, in most cases some user editing is required, because no system can remain selective while accounting for the full range of (anatomical) variation in nature or the occasional occurrence of preparation artifacts. This semi-automatic approach may improve altogether accuracy, objectivity and efficiency. Building chronologies of vessel size, for instance, can be sped up ten to twenty times without significant loss of accuracy (Fonti et al. 2009, see References). A key strength of ROXAS thus is to handle a wide range of suboptimal images in an efficient way (see sample images at the right side).

Features

• Processing of entire tree cores and cross-sections
• Automatic analysis of annual rings and conduits
• Efficient on-image editing of automatic results (deleting, drawing, adjusting, undoing)
• Analysis of tissue such as intervascular rays
• Selecting custom regions of interest (AOIs)
  
• Batch analysis (only full version, see Licensing)
• Adjustment of settings to specifics of samples
• Data output into well-organized MS Excel files (sample file, 627 KB)
  
• Reference manual
  

Output parameters (selection)

• Number of annual rings
• Width and area of annual rings
• Conduit number (globally and within annual rings)
• Conduit size (cross-sectional area)
• Conduit density (no./mm²)
  
• Vessel grouping index (sensu Carlquist)
  
• Affiliation of conduits to annual rings
• Relative / absolute conduit position within annual ring
• Hydraulic conductivity

Requirements

• Platform: Windows 2000 / XP / Vista / 7
• Software: Image-Pro Plus (Media Cybernetics) v4-7 (not 6.0!), MS Excel XP through 2010
• Performance: >=1 GB RAM, >=1.5 GHz
• image file formats: JPG, TIFF, BMP, PICT (color and grey scale)
  

Licensing

ROXAS is provided to the research community free of charge. It is delivered as a basic and a full version. The basic version of ROXAS is equivalent to the full version except for not providing any batch functions (see Features) and without any support. However, any published work that used ROXAS in part or all of analysis must refer to the proper citation, which is von Arx & Dietz 2005 (see References).

The full version of ROXAS (Pro) is bound to scientific collaboration with the author, Georg von Arx, in the corresponding project. 

Refer to the download link in the top right corner to obtain a setup file.

Sample images

If you want to try out ROXAS you may consider to download the data sets provided below. Just download the data set(s) and unzip the file. Then launch ROXAS, load the image file from the downloaded folder, and accept all suggested options. You will find the results of automatic ROXAS analysis at the end of this process.

• Data set 1: Sanguisorba minor, cross-section of root crown (30 µm), 0.63 pixels/µm (zip, 1.27 MB)
• Data set 2: Quercus petraea, tree core with surface imaging, 0.06 pixels/µm, courtesy of P. Fonti (zip, 1.27 MB)

References

• von Arx G, Archer SA, Hughes MK. 2012. Long-term functional plasticity in plant hydraulic architecture in response to supplemental moisture. Annals of Botany 109: 1091-1100. (Abstract)
  
• Fonti P, Eilmann B, Garcia-Gonzales I & von Arx G. 2009. Expeditious building of ring-porous earlywood vessel chronologies without loosing signal information. Trees – Structure and Function 23: 665-671.(PDF)
• von Arx G. 2006. A Tool for the Analysis of Annual Root Rings in Perennial Forbs. Media Cybernetics' Application Note (PDF)
• von Arx, G. 2005. Image-Pro Plus used to develop customized root cross-section analysis application. Media Cybernetics’ Customer Spotlight (PDF)
• von Arx G & Dietz H. 2005. Automated image analysis of annual rings in the roots of perennial forbs. International Journal of Plant Sciences 166: 723–732. (PDF)
  

Acknowledgement

So far, this project has been financially or logistically supported by:

• Velux Stiftung
• Geobotanical Institute ETH Zurich
  
• Schweizerische Botanische Gesellschaft
• Swiss Federal Institute for Forest, Snow and Landscape Research WSL

Contact

• Georg von Arx