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Palaeobotanical Tools

Preparation and Conservation
Managing Fossil Collections
Transfer Technique
Palynological Preparation Techniques
Cellulose Peel Technique
Latex Casts
Fluorescence Microscopy and Fluorescence Microspectroscopy
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)
Raman and Infrared Spectroscopy
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
Fluorescence Microscopy and Fluorescence Microspectroscopy
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)
Raman Spectroscopy
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.

! T. Alawsi and Z. Al-Bawi (2019): A review of smartphone point-of-care adapter design. Open access, Engineering Reports.

Andor Microscopy Techniques

! S. Asche et al. (2023): What it takes to solve the Origin (s) of Life: An integrated review of techniques. Free access, arXiv.
! Note figure 1: Comprehensive array of experimental and computational techniques, along with conceptual bridges, which are primarily utilised in OoL studies.
"... We review the common tools and techniques that have been used significantly in OoL [origin(s) of life] studies in recent years.
[...] it spans broadly — from analytical chemistry to mathematical models — and highlights areas of future work ..."

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.

Jeffrey B. Bindell, Department of Physics, University of Central Florida, Orlando, FL:
Optical Microscope (Introductory Comments on the Optical Microscope). Powerpoint lecture.

! V. Blahnik and O. Schindelbeck (2021): Smartphone imaging technology and its applications. Open access, Advanced Optical Technologies.

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.

The Canadian Nature Photographer, Calgary, Alberta, Canada.
This website provides a resource for learning about nature photography, art and great places to visit and photograph Nature both in Canada and around the world. Worth checking out:
Photoshop Workbook 1 and Photoshop Workbook 2 (in PDF).
! Robert Berdan (2020): The Microscopic Beauty of Plants and Trees. How to prepare and photograph plant sections for viewing with a microscope.

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.

J.M. Ede (2021): Deep learning in electron microscopy. Open access, Machine Learning: Science and Technology.

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.
30 Best Microscope Blogs and Websites in 2023.

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.

J.-P. Frahm (2012): Das Keyence VHX 500 Digitalmikroskop. In German.

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).

J. Götze et al. (2013): Optical microscope-cathodoluminescence (OM–CL) imaging as a powerful tool to reveal internal textures of minerals. In PDF, Mineralogy and Petrology, 106.
See also here.

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).

! B. Hunt et al. (2021): Smartphone-based imaging systems for medical applications: a critical review. Open access, Journal of Biomedical Optics.

! 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:

King Saud University (KSU), Riyadh, Saudi Arabia:
Optical Microscopy. Powerpoint presentation.

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, Proceedings of the Fine International Conference on Gigapixel Imaging for Science, November 11–13.
See also here.

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.
These expired links are now available through the Internet Archive´s Wayback Machine.

! S. McLoughlin et al. (2021): Neutron tomography, fluorescence and transmitted light microscopy reveal new insect damage, fungi and plant organ associations in the Late Cretaceous floras of Sweden. Open access, GFF, 143: 248-276.

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. (MSA)
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.

Microscope World, Carlsbad, CA.
! Microscope Information & Resources.
Measuring with a Microscope. (in German).
! Mikropraxis.
! Die Köhlersche Beleuchtung am Mikroskop einstellen.

Mikroskopie für Anfänger (in German). See especially "Linkliste zu Mikroskop-Themen".
The link is to a version archived by the Internet Archive´s Wayback Machine.

! (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.

Mohanlal Sukhadia University, Rajasthan, India:
A general introduction to Microscopy.
Powerpoint presentation.

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!

R.L. Mitchell et al. (2021): Correlative Microscopy: a tool for understanding soil weathering in modern analogues of early terrestrial biospheres. In PDF, Scientific Reports.

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.

David Neff, Marshall University, Huntington, WV:
Applied microscopy in research. See especially:
Microscopy. Powerpoint lecture.

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.
! Microscopy Resource Listings.

Olympus : Scientific Solutions.
Search for "microscopy".
Worth checking out:
! Olympus America Inc.: Specialized Microscopy Techniques. Available via Internet Archive Wayback Machine.
These websites contain information on light microscopy, e.g. fluorescence microscopy, transmission electron microscopes, contrast in optical microscopy and other imaging techniques.

! C.S. Pappas et al. ( 2003): New method for pollen identification by FT-IR spectroscopy. In PDF, Appl. Spectrosc., 57: 23-27. See also here.

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.

Quekett Microscopical Club, London, U.K.:
Microscopy. Websites directly related to microscopy.
! Links.

Quekett Microscopical Club, London, U.K.:
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.
These expired links are now available through the Internet Archive´s Wayback Machine.

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.

! S. Roy et al.(2014): Smartphone adapters for digital photomicrography. Open access, Journal of Pathology Informatics.

E.D. Salmon and Kerry Bloom, Biology department, The Bloom Lab, The University of North Carolina at Chapel Hil:
Light Microscopy and Electronic Imaging for the Biomedical Sciences. Powerpoint presentation.

! 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.

! A.C. Scott and M.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.
"Specimens were observed using transmitted light, polarized light, reflected light under oil, and cathodoluminescence. Selected areas were studied using a variable pressure SEM in backscattered electron mode. [...] Results reveal that anatomical interpretations based merely on observations of thin sections in transmitted light can be very misleading ..."

! 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.

A. Shinn (1996): To Make a Van Leeuwenhoek Microscope Replica. Free access, Microscopy Today.
See likewise here and there.

M. Somssich (2022): A Short history of plant light microscopy. Current Protocols, 2: e577. doi: 10.1002/cpz1.577

! 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, Microsc. Res. Tech. 81, 129–140.
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.

D.D. Vorontsov et al. (2023): Beyond the Limits of Light: An Application of Super-Resolution Confocal Microscopy (sCLSM) to Investigate Eocene Amber Microfossils. Open access, Life, 13(4), 865;
"... we describe a non-destructive method of super resolution confocal microscopy (sCLSM) to study amber-preserved microfossils ..."

D. Vorontsov and E.E. Voronezhskaya (2022): Pushing the limits of optical resolution in the study of the tiniest fossil arthropods. Abstract, Historical Biology.
"... we report our technical approaches and methodological findings, including the selection of mounting medium, clearing of specimens, the effects of hydration of fossils in amber and the advantages of super-resolution confocal microscopy in obtaining images with sub-micron detail. ..."

! Y. Wang et al. (2022): The Development of Microscopic Imaging Technology and its Application in Micro- and Nanotechnology. Open access, Front. Chem., 10:931169. doi: 10.3389/fchem.2022.931169.

Wikipedia, the free encyclopedia:
Category:Optical microscopy
! Köhler illumination.

! 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.
Websites still available via Internet Archive Wayback Machine.

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.

D. Yeloff and C. Hunt (2005): Fluorescence microscopy of pollen and spores: a tool for investigating environmental change. Abstract, Review of Palaeobotany and Palynology.

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. See especially:
! Microscope Alignment for Köhler Illumination.

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.

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 31, 2023

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