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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 (2015a). Methods for the analysis and illustration of morphometric data through geological time are given in Knappertsbusch (2000), Knappertsbusch (2001), Knappertsbusch (2009) [poster, pdf] and Knappertsbusch and Mary (2012).

 

 

 

 

AMOR - Automated Measurement system for shell mORphology

Updated 14 April 2020

 

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). AMOR has been eqipped with a specially designed close-range LED illumination ("Lagrangian illumination"), which avoids shadowing while tilting the specimens (FHNW student project Schneider & Chalençon, 2012).

 

The AMOR software was written in the graphical programming environment LabView from National Instruments, which is often used for prototyping in industrial automation. AMOR allows the operator to choose either the "single specimen mode" or the "automatic mode". In the "single specimen mode" the user can drive stage movements (x- and y-translation, x- and y-tilting), motorfocusing or magnification by mouse-clicks. In the "automatic mode" AMOR treats a multicellular slide equipped with foraminiferal specimens automatically, i.e. this fully automated robot moves microfossils, that are mounted in a standard slide, under the binocular, focuses on a specimen, tilts them in an optimum orientation, selects the ideal magnification, captures an image of the fossil, saves it to disk, and then advances to the next specimen until all objects are treated (Knappertsbusch et al., 2009). Further adaptation of the graphical user interface of AMOR allowed to drive AMOR by scripting, which gives even more flexibility for handling without the need of re-programming the LabView code (Mary, 2013).

 

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 collection of programs written in Fortran, see Knappertsbusch (2015a) and Knappertsbusch (2016).

 

In 2019 AMOR is was successfully duplicated and updated to System AMOR2, and routines for automated specimen orientation were improved, see Knappertsbusch, Eisenecker & Binggeli (2019a and 2019b), and Knappertsbusch and Eisenecker (2022).

 

• Download / see PowerPoint presentation EGU Vienna 7-12 April 2019 (screen presentation, Windows 10).
• Download poster presentation Swiss Geoscience Meeting Fribourg, 22nd-23rd Nov. 2019.

 

 

 

 

Completed projects leading hitherto to AMOR and related products:

 

Oegerli, K. (2015b). Software-Migration für Neubau Mikrofossilien-Abbildungsautomat AMOR. Bachelor-Thesis (Studienganf Systemtechnik, FHNW), 43 p. plus software. Supervision: Prof. S. Gaulocher (FHNW), customer: M. Knappertsbusch (NMB).

 

Oegerli, K. (2015a). Software-Anpassung für den Mikrofossilien-Abbildungsautomaten AMOR. Dokumentation P5 (Studienganf Systemtechnik, FHNW), 33 p. plus software. Supervision: Prof. S. Gaulocher (FHNW), customer: M. Knappertsbusch (NMB).

 

Scheffelmeier, J., Lescoeur, A., and Kaeser, M. (2014). AMOR Projekt (Automatisiertes Mess-System zur Untersuchung von Schalen MORphologien). Student project, Stage II des étudiants de la Formation Trinationale Mécatronique, 84 pages (text), plus CD Rom documentation. Supervision: Prof. J. Eisenecker (FHNW), customer: M. Knappertsbusch (NMB).

 

Schorpp, R. (2013). AMOR Software Beschreibung. Version 8.0. Auftragsarbeit FHNW. Unpublished report, 65 pages plus code. Customer: M. Knappertsbusch (NMB).

 

Schneider, E. and Chalençon, M. (2012). Machbarkeitsstudie für eine intelligente Beleuchtung für den Abbildungsautomaten AMOR. Student project. University of Applied Sciences (Fachhochschule Nordwestschweiz, FHNW), 14p. Supervisor: Prof. J. Eisenecker, FHNW; co-supervisor and customer: M. Knappertsbusch.

 

Strelcenko, A. (2011). Ueberarbeitung AVM 1.0. Automatische Vermessung von Mikrofossilien. Semestrial study, Institute for Automation, 22 p. Supervision: Prof. J. Eisenecker (FHNW), Customer: M. Knappertsbusch (NMB).

 

Unseld, A. (2010). Eigenform-Analysen für Mikrofossilien in AVM. Bachelor thesis (FHNW, Elektro- und Informationstechnik), 49 pages (text), plus code. Supervision: Prof. J. Eisenecker (FHNW), Expert: D. Faruggio, customer: M. Knappertsbusch.

 

Schorpp, R. (2010). AMOR Software Beschreibung. Version 3.0. Auftragsarbeit FHNW, 51 pages plus code. Customer: M. Knappertsbusch.

 

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, NMB.

 

Schorpp, R., Binggeli, D. und Eisenecker, J. (2009). Automatisches Messsystem für AMOR. Institut für Automation, FHNW Brugg/Windisch. Tätigkeitsbericht 2009, p. 30.

 

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. https://docplayer.org/11363706-Dokumentation-diplomarbeit-2830.html

 

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.

 

Binggeli, D. (2006). 4-Achs Mikroskoptisch für Mikrofossilien. Auftragsarbeit FHNW. Customer: M. Knappertsbusch. Unpublished documentation.

 

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.