Research: Tools for microfossil imaging and measurement

 

Geometric morphometry

 

We measure the morphological variability and evolution of selected calcareous marine microfossils. For this purpose and in the case of Neogene planktonic foraminifera digital images of the shells are taken through a microscope, and then analyzed using various morphometric methods (outline extraction, size and angular measurements of particular parameters, fourier decomposition of the outlines, see Knappertsbusch (1989) and Knappertsbusch (2004). Methods for the analysis and illustration of morphometric data through geological time are given in Knappertsbusch (2000), Knappertsbusch (2001), and Knappertsbusch (2009) [poster, pdf].

 

 

 

 

AMOR - Automated Measurement system for for shell mORphology

 

In order to have comparable results between specimens, the shells must be imaged in standard positions and orientations. Traditionally, this is achieved by manual positioning of a shell under the binocular using a hemispherical stage. This procedure is time-consuming if many specimens need to be studied for statistical analyses and results are influenced by the visual judgement of the researcher. In order to increase efficiency and precision of the measurements an automated positioning device called AMOR (from Automated Measurement system for for shell mORphology) was built during a series of bachelor student projects at the Institute for Automation, University of Applied Sciences of Northwestern Switherland (Fachhochschule Nordwestschweiz, FHNW). This work includes several versions of motorized stages for orientation and imaging of isolated microfossils under reflected light (Knappertsbusch et al., 2006). In the meantime we have at our disposition a fully automated robot, that moves microfossils, that are mounted in a standard slide, under the binocular, focuses it, tilts the specimen in an optimum orientation, selects the ideal magnification, and then captures an image of the fossil, saves it to disk, and advances to the next specimen until all objects are treated (Knappertsbusch et al., 2009). The collection of images obtained this way are processed to morphological parameters using additional software such as AVM (from Automatisierte Vermessung von Mikrofossilien, FHNW bachelor-thesis of Samuel Dietiker), or MorphCol, an earlier collection of programs written in Fortran (MorphCol, Knappertsbusch, 2004-2011).

 

 

Completed student projects leading to AMOR and related products:

 

Dietiker, S. (2009). Automatisierte Vermessung von Mikrofossilien. Bachelor-Thesis. University of Applied Sciences (Fachhochschule Nordwestschweiz, FHNW), 55 p. Chair: Prof. J. Eisenecker, FHNW; Experte: Dr. Ing. David Farrugio, co-supervisor and customer: M. Knappertsbusch.

 

Widmer, L. (2008). Automatische Zeichenerkennung- und Entfernung (Autocharacter) für AMOR. Bachelor-Thesis. University of Applied Sciences (Fachhochschule Nordwestschweiz, FHNW), 81 p. Chair: Prof. J. Eisenecker, FHNW; Experte: Dr. Ing. David Farrugio, co-supervisor and customer: M. Knappertsbusch.

 

Stapfer, S. (2007). Automatischer Vergrösserungswechsler (Auto-Zoom) und erweiterte Fokussierung für AMOR. Diploma thesis FHNW, 44 p. Chair: Prof. J. Eisenecker, FHNW; Expertin: M. Lefèbvre, co-supervisor and customer: M. Knappertsbusch.

 

Herzig, A. and Schmutz, L. (2007). Ansteuerung eines Mikroskops zur Untersuchung von Mikrofossilien. Diploma thesis FHNW, 64 p. Chair: Prof. J. Eisenecker, FHNW; Expertin: M. Lefèbvre, co-supervisor and customer: M. Knappertsbusch.

 

Degen, C. and Erni, A. (2005). Automatisierung der Mikrofossilienorientierung. Semestrial study (SS05) at the University of Applied Sciences (Fachhochschule beider Basel Nordwestschweiz, FHBB), Departement Industrie, Elektrotechnik und Informationstechnologie. 38 p. Chair: Prof. Dr. J. Kopainsky, co-supervisor and customer: M. Knappertsbusch.