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From AMOR to AMOR2 Prototypes for automated orientation and

From AMOR to AMOR2 Prototypes for automated orientation and Imaging of planktonic foraminifera for Morphometric analyses. Michael Knappertsbusch, Jean Eisenecker Natural History Museum Basel, Switzerland and Daniel Binggeli

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From AMOR to AMOR2 Prototypes for automated orientation and

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  1. From AMOR to AMOR2 Prototypes for automated orientation and Imaging of planktonic foraminifera for Morphometric analyses Michael Knappertsbusch, Jean Eisenecker Natural History Museum Basel, Switzerland and Daniel Binggeli Institut für Automation, Fachhochschule Nordwestschweiz Brugg-Windisch Michael.Knappertsbusch@unibas.chJean.Eisenecker@fhnw.chDaniel.Binggeli@fhnw.ch

  2. Contents A modifiedversionofthispresentation was presented at EGU General Assembly, Vienna, 7-12 April 2019 1. History 2. AMOR 3. AMOR 2 4. Scripting 5. Data extraction 6. Visualization Home

  3. History I Contents Controlling orientation of a single specimen Home Stage II Manual positioning under A binocular mikroskop and image collection Stage II

  4. History II Stage III – Addition of stepping motors Contents Home Single foraminifer

  5. History III Stage IV Motorized 4-Axis stage Contents X- and Y Tilt Home X- and Y Translation Multicellular slide

  6. GUI in manual mode. In automatic mode functions work in sequence for every field of the slide. Cross-polarized light Motorized focus „Lagrangian“ Illumination AX-Stand Digital videocamera (needs framegrabber) 4-Axis stage with slide holder for pitch (forward-backwards) and roll (left-right) movements. Software image rotation for vertical orientation of shells in keel-view LEDs move with specimens and so allow for constant illumination independent from tilting angle of stage. Motorized zoom (Can be disabled if necessary) AMOR Contents Home AMOR (from Automated system for the Measurement of shells for mORphometry)is a robot, that automatically orientates and images menardiform shells AMOR was built in collaboration with students and engineers of the University of Applied Sciences in Northwestern Switzerland. Programming environment is LabView from National Instruments.

  7. AMOR 2 Contents Home Twin just recentlyborn: Improvedsecond AMOR2

  8. AMOR 2 Hall-sensors @endpoints motor-zoom Digital JVC camera: IEEE 1394 interface (noframegrabber anylonger) New hardelements Contents Home Single box formotor Control stage & zoom Stage canbedisconnected fromstepper box and microscopeforbetter transportation.

  9. AMOR 2 Single mode: 1. Interactive numericalindicatorfields Forautomationfrom GUI. 2. Additional soft-rotation ofspecimen. Single mode: Automaticmagnification tomaximumsize. New soft elements Contents Single mode: Auto-Tilt Home Single mode: Orientatesymmetricorasymmetricforms Single mode: Auto soft-rotation intonorth- South orientation. Slide calibration: Movingleft-right, up-down Single mode: AutoFocusfunction in colormode

  10. AMOR 2 More soft elements Contents Automaticmode: Settings andselectionoffields. Home

  11. #cs ---------------------------------------------------------------------------- AutoIt Version: 3.3.6.0 Author: Yannick, Jean für Anpassung an AMOR 3.28 Script Function: Template AutoItscript. #ce ---------------------------------------------------------------------------- #include <GuiConstants.au3> ; Under Vista the Windows API "SetSystemTime" mayberejected due tosystemsecurity ;NOTE: AMOR parameters ; Average tilting time : 7 minutes ; ... ;note : thisversionhasbeencreatedfor Amor 3.28 ;CoortinatesofAMOR'songlets (ifupleftcorneris [0;0]) ;Initialization Global $detailuser[2] = [425, 326] Global $adjustlight[2] = [425, 368] Global $OkgotoAmor[2] = [497, 465] Global $Okmanuelmode[2] = [878, 173] ;Title: Settings singlemode Global $Loadcustom[2] = [90, 518] Global $entermanuel[2] = [93, 558] Global $save[2] = [458, 108] #cs ---------------------------------------------------------------------------- AutoIt Version: 3.3.6.0 Author: Yannick, Jean für Anpassung an AMOR 3.28 Script Function: Template AutoItscript. #ce ---------------------------------------------------------------------------- #include <GuiConstants.au3> ; Under Vista the Windows API "SetSystemTime" mayberejected due tosystemsecurity ;NOTE: AMOR parameters ; Average tilting time : 7 minutes ; ... ;note : thisversionhasbeencreatedfor Amor 3.28 ;CoortinatesofAMOR'songlets (ifupleftcorneris [0;0]) ;Initialization Global $detailuser[2] = [425, 326] Global $adjustlight[2] = [425, 368] Global $OkgotoAmor[2] = [497, 465] Global $Okmanuelmode[2] = [878, 173] ;Title: Settings singlemode Global $Loadcustom[2] = [90, 518] Global $entermanuel[2] = [93, 558] Global $save[2] = [458, 108] Scripting AMOR singlemode Scripting AMOR Contents Numericalindicators canberead All functionbuttons serveasinputfields andarescriptable Scripting sequenceoftasksusingAutoIt v. 3 By Jonathan Benett & AutoItteam www.autoitscript.com/ Autoit3/ Home

  12. Scripting AMOR singlemode Why Scripting ? High flexibility Using AMOR forotherforaminifera AvoidsLabViewprogramming Contents Home

  13. Batch processingof digital imagestoobtainoutlinecoordinates, determinationofosculatingcircles, dX, dY, area, keel-anglesand fourierspektra. Image: Knappertsbusch (2016). Swiss J. Palaeont. 135: 205-248 Fromimagesto Data:Extractionofmorphometricmeasurements Contents Home

  14. Guinea Basin Sample kindly provided from Stefan Müllegger . . . After processing: Data visualization Two examples for Holocene G. menardii Contents Home Guinea Basin Sample provided by Stefan Müllegger South-Atlantic Sample provided by Christiano Chiessi, University of Bremen

  15. Example- ODP Site 925BPhylogenyformenardiformgloborotalids G. menardii Contents G. multicamerata G. limbata Home PhylogenyfollowingKennett & Srinivasan (1983)

  16. Thanksforcontinuedsupportandcollaborationgoto: Swiss National Foundation (SNF) City of Basel Natural History Museum Basel Former groupof Prof. em. Jean Eisenecker and hisstudents (Institute of Automation, FHNW) Acknowledgements Contents Home

  17. Selected references. . . https://www.micropal-basel.unibas.ch Knappertsbusch, M., Binggeli, D., Herzig, A., Schmutz, L., Stapfer, S., Schneider, C., Eisenecker, J., and Widmer, L. (2009). AMOR – A newsystemforautomatedimagingofmicrofossilsformorphometricanalyses. PalaeontologiaElectronica 12(2); 2T. http://palaeo-electronica.org/2009_2/165/index.html Contents Mary, Y. (2013). Morphologic, biogeographicandontogeneticinvestigationof Mid-Pliocenemenardellids (planktonicforaminifera). Dissertation Univ. Basel. http://edoc.unibas.ch/diss/DissB_10611/ Knappertsbusch, M. (2015). MorphCol 2004-2013. A collectionofFortran 77 programsforgeometricmorphometry. Unpublished TechnicalReport, 1st Edition. Naturhistorisches Museum Basel, Switzerland. http://doi.pangaea.de/10.1594/PANGAEA.848773 Knappertsbusch, M. (2016). Evolutionaryprospection in the Neogene plankticforaminiferGloborotaliamenardiiandrelatedfroms from ODP Hole 925B (CearaRise, western tropicalAtlantic): evidencefor gradual evolutionsuperimposedbylongdistance dospersal ? Swiss Journal ofPalaeontology, 135(2):205-248. https://dx.doi.org/10.1007/s13358-016-0113-6 Home

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