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Palaeobotanical Tools

Preparation and Conservation
Managing Fossil Collections
Transfer Technique
Palynological Preparation Techniques
Cellulose Peel Technique
Latex Casts
Scanning- (SEM) and Environmental Scanning Electron Microscopy (ESEM)
Photography and Scanning
Digital Cameras on the Microscope
Cameras With Focus Bracketing or Built-In Focus Stacking
Focus Stacking (Photography, Extended Depth of Field)
High Dynamic Range Imaging (HDR)
Image Processing
Imaging Fossils Using UV-Light (Black-Light Photography)
Transmission Electron Microscopy (TEM)
Microtomography (CT Scanning, XTM) including Synchrotron X-ray Tomographic Microscopy (SRXTM)
Writing, Translating and Drawing

Home / Palaeobotanical Tools / Microscopy

Preparation and Conservation
Managing Fossil Collections
Palynological Preparation Techniques
Transfer Technique
Cellulose Peel Technique
Latex Casts
Scanning- (SEM) and Environmental Scanning Electron Microscopy (ESEM)
Photography and Scanning
Digital Cameras on the Microscope
Cameras With Focus Bracketing or Built-In Focus Stacking
Focus Stacking (Photography, Extended Depth of Field)
Superresolution (SR)
High Dynamic Range Imaging (HDR)
Image Processing
Imaging Fossils Using UV-Light (Black-Light Photography)
Transmission Electron Microscopy (TEM)
Microtomography (CT Scanning, XTM) including Synchrotron X-ray Tomographic Microscopy (SRXTM)
Writing, Translating and Drawing

! Chemotaxonomy and Chemometric Palaeobotany@
! Scientific Drawing@
Glossaries, Dictionaries and Encyclopedias: Microscopy@
Image Collections@
Picture Search@
Tutorials, Tips and Tricks to selected Writing and Drawing Computer Programs@
Grafic Software@

Microscopy (with Mary Bellis): Inventors, The History of the Microscope. Information from Newtom BBS, A Division of Educational Programs at Argonne National Laboratory and the National Institute of Health.

Andor Microscopy Techniques

A.D. Ball et al. (2016): Confocal microscopy applied to paleontological specimens. In PDF, The Paleontological Society Papers, 22: 39-55. See also here.

! M. Barrett et al., University of Delaware: Virtual microscope. The virtual microscope has all the same controls found on the real thing. Let Joelle introduce you to the microscope in a 7 minute video. Excellent!

Biozentrum Uni Basel und REM-Labor Uni Basel: Blockkurs Mikroskopie (in German).
Snapshot archived by the Internet Archive´s Wayback Machine.

! Alice Bergfeld (the English editor), Rolf Bergmann, University of Hamburg, and Peter v. Sengbusch, University of Bielefeld and Institut für Allgemeine Botanik, University of Hamburg: BOTANY Online - The Internet Hypertextbook. Botany online is based on the textbook "Botanik" by Peter von Sengbusch (Mc Graw Hill Book Company, 1989). Still available via Internet Archive Wayback Machine.

! BiologyBrowser (produced by Thomson Scientific). This is a free web site offering resources for the life sciences information community.

Bruce Bryson, From Quarks to Quasars. On the relative size of things and the question of scale. This is a visual journey consisting of 42 images, 42 powers of ten. At one end of the journey is the immensity of the known universe, some 15 000 000 000 years old and 10 to 20x109 light years across. At the other end of the journey is a depiction of the three quarks within a proton.

Department of Materials Science and Metallurgy, University of Cambridge: Optical Microscopy and Specimen Preparation. This teaching and learning package provides an introduction to the use of optical microscopes. It introduces the different types of microscope used to examine specimens and how to set them up correctly. There is also an introduction to specimen preparation.
This expired link is available through the Internet Archive´s Wayback Machine.

N.D.L. Clark and C. Daly (2010): Using confocal laser scanning microscopy to image trichome inclusions in amber. In PDF, Journal of Paleontological Techniques, 8: 1-7. See also here.

T.J. Collins (2007): ImageJ for microscopy. In PDF, Biotechniques.
The link is to a version archived by the Internet Archive´s Wayback Machine.

Russ Crutcher: MicrolabNW Photomicrograph Gallery.
Thousands of particles under the microscope. You can navigate from the Category Index. Worth to check out:
! Pollen.

! M.W. Davidson and T.J. Fellers Understanding conjugate planes and Köhler illumination. In PDF.

Michael W. Davidson and the Florida State University (in collaboration with Optical Microscopy at the National High Magnetic Field Laboratory): Science, Optics and You: Powers of 10. Interactive java tutorial journeys in stages from 10 million light years beyond the Milky Way to a treetop to the nucleus at the heart of an atom, in order to visually describe orders of magnitude.

Michael W. Davidson, Institute of Molecular Biophysics, Center for Materials Research and Technology (MARTECH), National High Magnetic Field Laboratory (NHMFL), Supercomputer Computations Research Institute (SCRI), Florida State University, Tallahassee, and Gary E. Lofgren, Planetary Materials Branch, Solar System Exploration Division, NASA Johnson Space Center, Houston, Texas: Photomicrography in the Geological Sciences. In this article the authors describe the conversion of a standard biological brightfield microscope for examination of geological petrographic thin sections and characterize, in detail, the use of both black and white and color photomicrography in the geological sciences. Several illustrative examples on the use of transmitted and reflected polarized light microscopy to solve geological problems are presented.

Michael W. Davidson, Mortimer Abramowitz, Olympus America Inc., and The Florida State University: Molecular Expressions, Introduction to Optical Microscopy, Digital Imaging, and Photomicrography.

Dissemination of IT for the Promotion of Materials Science (DoITPoMS), Department of Materials Science and Metallurgy, University of Cambridge: Optical Microscopy and Specimen Preparation. This teaching and learning package provides an introduction to the use of optical microscopes. It introduces the different types of microscope used to examine specimens and how to set them up correctly. There is also an introduction to specimen preparation.

eLS. Citable reviews in the life sciences (Wiley). eLS features peer-reviewed articles in the life sciences, written by leaders in the field to provide comprehensive and authoritative coverage of each subject area. Go to:
! Microscopy.

! H.J. Falcon-Lang and D.M. Digrius (2014): Palaeobotany under the microscope: history of the invention and widespread adoption of the petrographic thin section technique. In PDF.

H. Falcon-Lang (2012): Double-crossed Nicol. William Nicol pioneered petrographic microscopy; but a dastardly palaeobotanist tried to steal his glory.

! Susanne Feist-Burkhardt, Institute for Geology and Palaeontology Darmstadt University of Technology, Germany and Jörg Pross Institute and Museum for Geology and Palaeontology, University of Tübingen, Germany (website hosted by The Natural History Museum, London): Confocal Laser Scanning Microscopy (CLSM) and its application to fossil dinoflagellate cysts.

Electron Microscopy Core Laboratory (EMCL), Biotechnology Program, University of Florida, Gainesville, FL: Tips & Tricks. This information is gleaned from the Microscopy and Confocal list-servers as well as from independent contributions. Snapshot taken by the Internet Archive´s Wayback Machine. Go to:
Light Microscopy, and SEM.

M. Frese et al. (2017): Imaging of Jurassic fossils from the Talbragar Fish Bed using fluorescence, photoluminescence, and elemental and mineralogical mapping. PLoS ONE 12(6): e0179029.
"... Closer inspection of a plant leaf (Pentoxylon australicum White, 1981) establishes fluorescence as a useful tool for the visualisation of anatomical details that are difficult to see under normal light conditions".

! O. Gavrilova et al. (2017): Potential of CLSM in studying some modern and fossil palynological objects. Abstract, Journal of Microscopy, 00: 1–19. See also here and there (in PDF).

O.R. Green (2013): A Manual of Practical Laboratory and Field Techniques in Palaeobiology. Google books.

! Alan Hadley, U.K.: CombineZ5 (still available, because it works with older versions of windows), and CombineZ Movie (CZM). The purpose of these free programs is to increase depth of focus by combining pictures, but each picture should be in focus at a different depth into the scene. The programs are especially useful to microscope users (fluid inclusions!) and macro photographers. Excellent! CZM is the latest version, it can process movies, take pictures, and has more macro commands but still has all of the functionality of CombineZ5.
See also here (about Interactive Digital Photomontage), and a review of Helicon Focus and CombineZ5 software (by John Hollenberg, Digital Outback Photo).

J.T. Haug et al. (2011): Autofluorescence imaging, an excellent tool for comparative morphology. In PDF, Journal of Microscopy.

! Klaus Henkel (2003): Die Mikrofibel. All about microscopy (PDF file, in German).

! ImageJ: ImageJ is an open source image processing program for multidimensional image data with a focus on scientific imaging. See also here. Don´t miss the
! List of update sites Also worth checking out:
! Tutorials and Examples.
ImageJ (from Wikipedia, the free encyclopedia).
C.A. Schneider et al. (2012): NIH Image to ImageJ: 25 years of image analysis. In PDF, Nature methods.

T. Itaki et al. (2020): Automated collection of single species of microfossils using a deep learning–micromanipulator system. Open access, Progress in Earth and Planetary Science, 7.

Keyence. A leading supplier of digital microscopes, as well as sensors, measuring systems, laser markers, etc. Go to:

Heather Kroening, & Karen Hagen, Department of Biological Sciences, University of Alberta: Instructional Multimedia, Multimedia Topics, Procedures. Go to: Parts of the Microscope, How to make a wet mount. Online and downloadable flash movies.

Leica Microsystems. Go to: Leica Microsystems, Downloads: Editorial Articles.

Lightscapes Webring. Website dedicated to polarized light microscopy.

Z.-J. Liu and X. Wang (2016): A perfect flower from the Jurassic of China. In PDF, Historical Biology, 28: 707-719. See also here (Abstract).

! Jay Longson et al. (2010): Adapting Traditional Macro and Micro Photography for Scientific Gigapixel Imaging. PDF file, Fine International Conference on Gigapixel Imaging for Science.

Timo Mappes, Institut für Mikrostrukturtechnik, Forschungszentrum Karlsruhe GmbH, Karlsruhe, Germany: Museum of Optical Instruments (in German). This website provides information about the history of scientific instrumentation, as well as information about their makers.

James Mayer, Arizona State University, Tempe, and Daniel Adams, University of the Western Cape, South Africa: Images of Nature. Microscopic images. This is an educational site created as a tool for science educators, including quizzes about the images (SEM, EDS, PIXE, and Optical) as well as spectral data (PIXE and EDS). Go to: The Basics of Image Analysis Techniques. Introductions to optical microscopy and X-ray analysis.

Microscopy Today (owned by the Microscopy Society of America). Editorial coverage of Microscopy Today spans all microscopy techniques including light microscopy, scanning probe microscopy, electron microscopy, ion-beam techniques, and the wide range of microanalytical methods.

Microscopy Society of America. The Microscopy Society of America (MSA) is a non-profit organization dedicated to the promotion and advancement of the knowledge of the science and practice of all microscopical imaging, analysis and diffraction techniques useful for elucidating the ultrastructure and function of materials in diverse areas of biological, materials, medical and physical sciences.

Mikro-Forum (Christian Linkenheld, Oppenau). In German. Please take notice:
! Links and literature about microscopy.

! Mikroskopedia (by MC Services). Microscopy and Microanalysis news, events, companies, laboratories, societies, web resources, products and more. Go to: Web Resources.

Mikroskopie für Anfänger (in German). See especially "Linkliste zu Mikroskop-Themen".

! (website hosted by edv-marketing & mediadesign, Göttingen). Microscopy in a nutshell, a German forum.

Center For Interfacial Engineering, University of Minnesota: Standard Microscopy Terminology. This is a compilation of glossaries from "Glossary of Microscopical Terms and Definitions" (New York Microscopical Society), and "Video Microscopy" by Shinya Inoue, 1986, third printing, Plenum Press, New York.
Now recovered from the Internet Archive´s Wayback Machine.

University of Missouri-St. Louis, St. Louis, Missouri: Other Microscopy/Interesting Sites Around the World.

Molecular Expressions (in collaboration with Optical Microscopy at the National High Magnetic Field Laboratory, Florida State University): Exploring the World of Optics and Microscopy, and Microscopy Primer, Introduction to Microscopy. This treatise on Microscopy is divided into several sections, e.g. specialized microscopy techniques, anatomy of the microscope, the 50 most commonly asked questions about microscopy and photomicrography, web resources etc. Visit the Interactive Java Tutorials. These virtual microscopes explore specimen focus, illumination intensity, magnification, and translation, operating essentially in a manner that is identical to real-life microscopes. Excellent!

D. Moore (2000): Setting up the microscope, part 1. In PDF, Field Mycology 1.
D. Moore (2003): Setting up the microscope, part 2. In PDF, Field Mycology 4.

Nikon Microskopyu.
Worth checking out: Basic Concepts and Formulas in Microscopy.

! Nobel e-Museum, The Nobel Foundation, Sweden: Microscopes – Help Scientists Explore Hidden Worlds. Information about Phase Contrast-, Fluorescence-, Transmission Electron-, and Scanning Tunneling Microscopes, (including a microscopy time line), as well as interactive simulators.

! R.J. Oldfield (2001): Differential Interference Contrast Light Microscopy. In PDF. See also here and there.

Olympus Industrial America Micro-Imaging Division.

! Olympus America Inc.: Specialized Microscopy Techniques. These websites contain information on light microscopy, e.g. fluorescence microscopy, transmission electron microscopes, contrast in optical microscopy and other imaging techniques.

Susanne Pignolet Brandom, MicroWorld Resources and News: An Annotated Guide to On-line Resources for Microscopists and Other Scientists.

M.E. Popa (2011): Field and laboratory techniques in plant compressions: an integrated approach. In PDF, Acta Palaeontologica Romaniae. See also here and there.

! The Quekett Microscopical Club. An organisation for all who are interested in the microscope and microscopy. Go to:
Advanced Digital Photomicrography.
A version archived by the Internet Archive´s Wayback Machine.
Also worth checking out: Glossary.

! Philip D. Rack, Dept. of Materials Science and Engineering, University of Tennessee: Materials Laboratory Procedures. Go to:
Optical Microscopy, and Sample Preparation (PDF files).
The nuts and bolds of microscopy, including hints about sample preparation.

Radboud University, Nijmegen, The Netherlands: Virtual Classroom Biology. This website is an educational site, especially meant for secondary school students who like to have a first glance on teaching items of the Bio-science programs. One can find custom-made teaching material for courses from the biology training. Navigate from here. See especially:
Light microscopy techniques.
Electron microscopy (EM).

E. Romero et al. (2007): Virtual Microscopy in Medical Images: a Survey. In PDF.

! J. Sanderson (2002): Practical control of contrast in the microscope. Quekett Journal of Microscopy, 39: 275–288.

SCANNING. Scanning provides an international and interdisciplinary medium for the rapid exchange of information among all scientists interested in scanning electron, scanning probe, and scanning optical microscopies.

K. Schollaen et al. (2014): UV-laser-based microscopic dissection of tree rings - a novel sampling tool for d13C and d18O studies. In PDF, New Phytologist, 201: 1045–1055.

P. Schols et al. (2010): CARNOY: A new digital measurement tool for palynology. In PDF, Grana, 41: 124-126.

SciCentral. Go to: Microscopy.

! Andrew C. Scott and Margaret E. Collinson (2003): Non-destructive multiple approaches to interpret the preservation of plant fossils: implications for calcium-rich permineralisations. PDF file, Journal of the Geological Society, 160: 857-862. See also here.

! C.S. Shi et al. (2013): Characterization of the stem anatomy of the Eocene fern Dennstaedtiopsis aerenchymata (Dennstaedtiaceae) by use of confocal laser scanning microscopy. Free access, American Journal of Botany, 100: 1626–1640.

Alan Shinn, Berkeley: To Make a Van Leeuwenhoek Microscope Replica. This web site provides full plans for developing a van Leeuwenhoek-like microscope. See also: Microscope use instructions.

! M. Speranza et al. (2010): Traditional and new microscopy techniques applied to the study of microscopic fungi included in amber. PDF file, In: A. Méndez-Vilas and J. Díaz (eds.): Microscopy: Science, Technology, Applications and Education. Scanning electron microscopy in backscattered electron mode, with energy dispersive X-ray spectroscopy microanalysis.
Now recovered from the Internet Archive´s Wayback Machine.

B.A. Thomas et al. (2004): Palaeobotanical applications of incident-light darkfield microscopy. In PDF, Palaeontology 47: 1641-1645. See also here.

M.A. Urban et al. (2018): Cuticle and subsurface ornamentation of intact plant leaf epidermis under confocal and superresolution microscopy. In PDF, See also here and there.

Wim van Egmond, Micscape Magazine, U.K.: An Introduction to Microscopy. In the following pages you will get information about the microscope and about the subjects you can study with. Further links direct you to many articles that appeared in the monthly web magazine Micscape.

! Wikipedia, the free encyclopedia:
Bright field microscopy.
Confocal microscopy.
Category: Microscopy. List of materials analysis methods.

The Wilson Group, University of California, San Diego: The World of Physical Chemistry, Spectroscopy. Go to Introduction to Spectroscopy and Polarization.

Stephen M. Wolniak, Department of Cell Biology & Molecular Genetics, University of Maryland: Principles of Microscopy.

! WWW-Virtual Library: Microscopy links. Aspects of light microscopy, electron microscopy and other forms of microscopy.

Dan Yeloff and Chris Hunt (2004): Fluorescence microscopy of pollen and spores: a tool for investigating environmental change. Abstract.

Nestor J. Zaluzec, (page hosted by the AAEM and TPM Projects at Argonne National Laboratory): ANL Microscopy and Microanalysis WWW Server. A good list of links to other microscopy sites. Worth to visit: PDF Slides/Lecture Notes of short courses.

Carl Zeiss, Oberkochen:
! Education in Microscopy and Digital Imaging. Tutorials and introductions about the fascinating world of optical microscopy. Worth checking out:
Microscopy Reference Library. Books, review articles, and original research reports that deal with numerous topics in optical microscopy.

Carl Zeiss MicroImaging GmbH: Microscopy from the very beginning.
Provided by the Internet Archive´s Wayback Machine.

Carl Zeiss Microscopy: Microscope Software AxioVision LE (AxioVision LE for Windows, available as 32-bit and 64-bit version). Freeware imaging software for image analysis and digital microscopy.
See also: Microscopy.

Hans Dieter Zimmermann, Geologisk Institut, Aarhus Universitet, Århus, Denmark: Polarisationsmikroskopi. In Danish.

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This index is compiled and maintained by Klaus-Peter Kelber, Würzburg,
Last updated February 06, 2021

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