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Palaeobotanical Tools

Preparation and Conservation
Transfer Technique
Palynological Preparation Techniques
Cellulose Peel Technique
Latex Casts
Photography and Scanning
Digital Cameras on the Microscope
Focus Stacking (Photography, Extended Depth of Field)
High Dynamic Range Imaging (HDR)
Image Processing
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
Palynological Preparation Techniques
Transfer Technique
Cellulose Peel Technique
Latex Casts
Photography and Scanning
Digital Cameras on the Microscope
Focus Stacking (Photography, Extended Depth of Field)
Superresolution (SR)
High Dynamic Range Imaging (HDR)
Image Processing
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

! Elizabeth B. Andrews (2009): Windows on a Lilliputian world: a personal perspective on the development of electron microscopy in the twentieth century. PDF file, Notes Rec. R. Soc. See also here.

! BiologyBrowser (produced by Thomson Scientific). This is a free web site offering resources for the life sciences information community. Go to: Subject > Methods and Techniques > Paleontological techniques.

Biozentrum Uni Basel und REM-Labor Uni Basel: Blockkurs Mikroskopie (in German).

Alice Bergfeld (she is the English editor), Rolf Bergmann, University of Hamburg, and Peter v. Sengbusch, University of Bielefeld and Institut für Allgemeine Botanik, University of Hamburg: Microscopy. Part of BOTANY Online - The Internet Hypertextbook.

! Derek Briggs and Peter Crowther (eds.), Earth Pages, Blackwell Publishing: Paleobiology: A Synthesis (PDF files). Series of concise articles from over 150 leading authorities from around the world. Navigate from the content file. Excellent! Go to: Infrastructure of Palaeobiology.

Chris Jefferies, Bristol: Microscopes and Microscopy. An extensive index of microscopy sources on the web, listed by geographical locations, organisations, and subject. Very useful!

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.

Angelo Capparella and Martha Cook, llinois State University: Biological Diversity. Navigate from here (PowerPoint Presentations). The subject matter of the course will provide an overview of biological diversity emphasizing major innovations in structure and function, including ecology and physiology, as well as the phylogeny (evolutionary history) and systematics (e.g., taxonomy) of living organisms. Go to: Microscopy (in ppt).

John W. Cross, Missouri Botanical Garden: Scanning Probe Microscopy (SPM). See also here (without frames).

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.

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.

dmoz open directory project: Top: Science: Methods and Techniques: Microscopy.

John Donovan, Micro Analytical Facility, CAMCOR Center for Advanced Materials Characterization in ORegon, University of Oregon, Eugene: Electron Microscopy Societies and On-line Journals, and EPMA & SEM facilities, World Wide.

! 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.

A. Fels, Fels Werkstoffanalytik, Stuttgart: Grundlagen der Raster-Elektronenmikroskopie mit Schwerpunkt Sedimentpetrographie. A tutorial (in German). See also: Literatur zur Raster-Elektronenmikroskopie.

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. Go to: Light Microscopy, and SEM.

! 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.

! Helicon Soft Ltd., Kharkov, Ukraine: Helicon Focus. This is a shareware program that creates a completely focused image from several partially focused images by combining the focused areas. You can download and use the program for evaluation purposes for 30 days. Helicon Focus is designed for macrophotography, microphotography (fluid inclusions!) and hyperfocal landscape photography to cope with the shallow depth-of-field problem. Excellent!
See also here, and there (in German).

University of Idaho: Mickey´s Web Page. Research, teaching, and fun in optical mineralogy.

JEOL-USA, Inc., Peabody, MA: JEOL is an innovator in developing instruments used in advanced scientific research and technology (electron microscopy, mass spectrometry, e-beam lithography and defect analysis). Go to:
! A Guide to Scanning Microscope Observation (HTML or PDF).

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.

Lance Ladic, Dept. of Physiology, (Imager Computer Graphics Laboratory (IMAGER), Department of Computer Science), University of British Columbia, Vancouver: 3-D Laser Scanning Confocal Microscopy (LSCM, also referred to as CSLM, Confocal Scanning Laser Microscopy).

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

Lightscapes Webring. Website dedicated to polarized light microscopy.

Department of Mineralogy, The Natural History Museum, London: Electron microscopy and mineral analysis. Techniques include electron probe microanalysis, inductively coupled plasma spectrometry, laser ablation inductively coupled plasma mass spectrometry, transmission electron microscopy, cathodoluminenscence etc.

! 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.

Erhard Mathias, Germany: Micro Contrasts. Methods for the optimization of light microscopy.

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 Information. This website contains articles on a range of microscopy related topics, e.g. the maintenance of microscope parts, microscope optics and theory, sample preparation and microscope techniques. (in German).

John F. Mansfield, University of Michigan, Electron Microbeam Analysis Laboratory & The Department of Materials Science & Engineering: Microscopy Web Sites Around the World, and Microscopy Societies.

Microscopy Online is a free hyper-journal published on the World Wide Web designed specifically for the microscopist. Registration required.

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.

MicroWorld Resources and News, Guide to Microscopy and Microanalysis on the Internet: Image Analysis, Image Processing, and 3-D Reconstruction. Link page of FAQs, meta lists, online tutorials, and source code links.

MicroWorld, Guide to Online Microscopy and Microanalysis Resources. MicroWorld Resources, Electron Microscope Links. Including Introductory Information, Lecture Notes, Imaging, AEM, HRTEM, and TEM Techniques, 3-D Electron Microscopy, SEM Techniques, Electron Microscopy Courses and Training, Remote Microscopy, More Helpful Sites, and Manufacturers WWW sites.

MicroWorld: MicroWorld Resources and News. An annotated guide to online resources for microscopists and microanalysts.

MicroWorld: Microscopy Vendors and Suppliers. Analytical services, laboratories, education and training.

MicroWorld: Glossary of Microscopy and Microanalytical Terms. Index page about general microscopy glossaries, confocal and laser microscopy, electron beam techniques, light microscopy, imaging, mass spectrometric, nucear magnetic microscopy, scanning probe microscopy, spectrometry-accelerator and X-ray microscopy.

! (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.

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!

Nuno Moreno et al. (2006): Imaging Plant Cells. PDF file, Handbook of Biological Confocal Microscopy, third edition, edited by James B. Pawley.

Udo Neumann, Institut für Geowissenschaften der Universität Tübingen Auflichtmikroskopie und Erzpetrographie. Some hints and citations about reflected light and ore microscopy (in German).

Nikon: Coolscope. An all in one microscope, performed with simple mouseclicks (?)

! Nikon Microscopy. Some optical microscopy tutorials. Go to:
Basic Concepts and Formulas in Microscopy,
Principles of Phase Contrast Microscopy,
Concepts in Fluorescence Microscopy, including Introduction to Fluorescence Microscopy, and
Fundamental Concepts in Confocal Microscopy. Superbly done!

! 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.

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.

! Imogen Poole and Geoffrey E. Lloyd (2000): Alternative SEM techniques for observing pyritised fossil material. PDF file, Review of Palaeobotany and Palynology 112: 287-295.

! 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.

! Philip D. Rack, Dept. of Materials Science and Engineering, University of Tennessee: Materials Laboratory Procedures. Go to:
Scanning Electron Microscopy (PDF file).

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).

Melissa B. Riley, Department of Plant Pathology and Physiology, Clemson University (site is maintained by American Phytopathological Society): Basic Microscopy - An Important Skill for Plant Pathologists. A basic tutorial: Becoming familiar with the components of microscopes and the steps for proper focusing and how to determine the magnification of materials being observed using a microscope.

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

Information Technology Department, the UCSD Libraries and Academic Computing Services. University of California, San Diego: Web Course Notes and References, Principles of the Transmission Electron Microscope (TEM).

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.

SciCentral. Go to: Microscopy.

Science Learning Network (SLN): Scanning Electron Microscope. SLN is an online community of educators, students, schools, science museums and other institutions demonstrating a new model for inquiry science education.

! 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.

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. In PDF, In: A. Méndez-Vilas and J. Díaz (eds.): Microscopy: Science, Technology, Applications and Education. See also here.

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

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.

Giuseppe Vicidomini et al. (2008): High Data Output and Automated 3D Correlative Light-Electron Microscopy Method. In PDF.

! 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.

YAHOO: Science > Engineering > Optical Engineering Microscopy. 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.

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

Carl Zeiss MicroImaging GmbH: Microscopy from the very beginning.

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 December 10, 2014

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