Links for Palaeobotanists

Home / Palaeobotanical Tools / Digital Image Processing

Preparation and Conservation
Managing Fossil Collections
Transfer Technique
Palynological Preparation Techniques
Cellulose Peel Technique
Latex Casts
Photography and Scanning
Fluorescence Microscopy and Fluorescence Microspectroscopy
Scanning- (SEM) and Environmental Scanning Electron Microscopy (ESEM)
Imaging Fossils Using UV-Light (Black-Light Photography)
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)
Transmission Electron Microscopy (TEM)
Microtomography (CT Scanning, XTM) including Synchrotron X-ray Tomographic Microscopy (SRXTM)
Raman Spectroscopy
Writing, Translating and Drawing

Glossaries, Dictionaries and Encyclopedias: Microscopy@
! Scientific Drawing@
! Chemotaxonomy and Chemometric Palaeobotany@

Digital Image Processing Desktop Publishing. This site offers writing tips, desktop publishing tutorials and information about desktop publishing software.
Snapshot provided by the Internet Archive´s Wayback Machine.

! A. Agarwala et al.: Interactive Digital Photomontage. In PDF. See also here.

! Georg von Arx et al. (2016): Quantitative Wood Anatomy Practical Guidelines. Free access, Front. Plant Sci., 7.
See also here.

Paul A. Barber and Philip J. Keane (2007): A novel method of illustrating microfungi. PDF file, Fungal Diversity, 27: 1-10.
Snapshot archived by the Internet Archive´s Wayback Machine.

Dee Breger (The Silicofossil Group, The Micropalaeontological Society TMS):
Colouring-in micrographs - bringing images from the cloistered lab to the general public. See also:
Gallery. Some false coloured images.
Still available via Internet Archive Wayback Machine.

S.M. Bybee and M.A. Branham (2008): Scanning Rocks for Data. In PDF, American Entomologist.

Cambridge in Colour: This is an online learning environment where photographers can come to improve their skills.
! Sharpness Tutorial.

Karen Carr, Karen Carr Studio, Silver City, NM:
You Can Paint Digitally!
This expired link is now available through the Internet Archive´s Wayback Machine.

E. Frow (2012): Drawing a Line: Setting Guidelines for Digital Image Processing in Scientific Journal Articles Social Studies of Science, 42: 369-392.

! J.A. Cunningham et al. (2014): A virtual world of paleontology. Trends in Ecology & Evolution, 29: 347-357.

! E.M. Friis et al. (2013): New Diversity among Chlamydospermous Seeds from the Early Cretaceous of Portugal and North America. Free accesss, International Journal of Plant Sciences, 174: 530558.
"... The material is based on numerous charcoalified and lignitic specimens recovered from Early Cretaceous mesofossil floras [...]
! Attenuation-based synchrotron-radiation x-ray tomographic microscopy (SRXTM) and phase-contrast x-ray tomographic microscopy (PCXTM) were carried out [...]
! Volume rendering (voltex), which provides transparent reconstructions, was also used for the virtual sections ..."

C. Haug et al.: New Methods to Document Fossils from Lithographic Limestones of Southern Germany and Lebanon. PDF file, Palaeontologia Electronica Vol. 12. About composite imaging.

Richard Hill, Lunar and Planetary Lab, University of Arizona: Experiments in scanning fossils. Examples. The trick is to select small areas in the scanning software and then use the highest resolution.

The Image: Gifology. Understanding GIF files and GIF animation.

! 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. Digital image processing books and other educational resources. Go to: Tutorials. All downloadable files in this site are compressed in zip format.

T.S. Karim et al. (2016): Digitization workflows for paleontology collections. Palaeontologia Electronica.

S. Lautenschlager (2016): Reconstructing the past: methods and techniques for the digital restoration of fossils. Abstract, R. Soc. sci., 3. See also here (in PDF).

! H. Mallison (2012): Digitizing Methods for Paleontology: Applications, Benefits and Limitations. In PDF, in: A.M.T. Elewa (ed.), Computational Paleontology, pp 743.
See also here.

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.
Now provided by the Internet Archive´s Wayback Machine.

G. Montesanto (2015): A fast GNU method to draw accurate scientific illustrations for taxonomy. Zookeys, 515: 191206.

G. Nelson and S. Ellis (2018): The history and impact of digitization and digital data mobilization on biodiversity research. Free access, Phil. Trans. R. Soc. B, 374: 20170391.
See also here.
"... The recent expansion of digital data has placed biodiversity collections on the cusp of big data science, opening multiple pathways for natural history museums ..."

! A.J. North (2006): Seeing is believing? A beginners´ guide to practical pitfalls in image acquisition. See also here (in PDF).

R. Pan and V. Skala (2013): Normal map acquisition of nearly flat objects using a flatbed scanner. In PDF, 2013 International Conference on Virtual Reality and Visualization.
See also here.

! R. Pintus et al. (2019): State-of-the-art in Multi-Light Image Collections for Surface Visualization and Analysis In PDF, Computer Graphics Forum, 38. See also here.
"... Multi-Light Image Collections (MLICs), i.e., stacks of photos of a scene acquired with a fixed viewpoint and a varying surface illumination
[...] We [...] review techniques that improve object understanding by using illustrative approaches
[...] We also review how these methods are applied in several, main application domains, and what are the available tools to perform MLIC visualization and analysis. We finally point out relevant research issues, analyze research trends, and offer guidelines for practical applications ..."

M.P. Pound et al. (2017): Deep Machine Learning provides state-of-the-art performance in image-based plant phenotyping. GigaScience. See also here (in PDF).

! K.M. Pryer et al. (2020): Using computer vision on herbarium specimen images to discriminate among closely related horsetails (Equisetum). Open access, Applications in plant sciences, 8.

E. Reeves et al. (2023): Historic palaeobotanical collection reveals in situ microspores and pollen from Early Carboniferous (Tournaisian) ovules from the Ballagan Formation of Scotland. Free access, Review of Palaeobotany and Palynology, 308.
"... The resultant 67 photomicrographs were photo-stitched into one large image
[...] Single microspores and pollen within the ovule were photographed under oil at ×100 using multiple images at different focus depths and then Z-stacked ..."

J.B. Riding and M.J. Head (2017): Preparing photographic plates of palynomorphs in the digital age. Palynology, 42. See also here (in PDF).

! G. Rossetto-Harris et al. (2022): Rapid character scoring and tabulation of large leaf-image libraries using Adobe Bridge. Open access, Appl. Plant Sci., 10: e11500.
Note figure 1: Flowchart illustrating the workflow to annotate large image libraries.
"... Our approach is intuitive and acts as a digital mimic and complement to the experience of sorting and analyzing specimens in-person. Keywords can be easily customized for other data types that require visual sorting using image libraries ..."

! Mike Rossner and Kenneth M. Yamada (2004): What´s in a picture? The temptation of image manipulation. In PDF, J. Cell Biol., 166: 11-15.

! M. Schädel, University of Tuebingen: Multi Light Imaging of small compression fossils proper tools and a neat shortcut. In PDF, Conference poster: The Palaeontological Association 67th Annual Meeting, University of Cambridge, UK.
About Multi Light Imaging with focus stacking or panoramic stitching.

Volker Schardin: Extensions/Suffixes (in German). Index to the most used extensions.
This expired link is available through the Internet Archive´s Wayback Machine.

! J. Schindelin et al. (2012): Fiji - an Open Source platform for biological image analysis. Open access, Nat Methods, 9: 10.1038/nmeth.2019.

C.A. Schneider et al. (2012): NIH Image to ImageJ: 25 years of image analysis. In PDF, Nature methods.

! P.A. Selden (2014): A workflow for digital photography of fossil specimens. In PDF, The Geological Curator, 10: 93-97.

! Seam Carving GUI. Seam carving for content-aware image resizing. Free download! Also available as online tool.
For more see here, and there (Wikipedia), or read about the nuts and bolts (PDF file, by Shai Avidan (Mitsubishi) and Ariel Shamir, ACM Transactions on Graphics, Volume 26).

! Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, D.C.: Paleo Art. This website provides information about taking proper care of illustrations and discusses techniques for creating palaeontological and other scientific illustrations. Go to:
! What is paleontological illustration, and Illustration Care. To provide archival care (conservation treatment) for historical illustrations. Don´t miss the
Historical Art Gallery and the Bibliography of Historical Art. Some highlights from the Department of Paleobiology. Last but not least:
! Reconstructing an ancient environment. Reconstructing of invertebrates, vertebrates and fossil plants.
These expired links are now available through the Internet Archive´s Wayback Machine.

U.S. Geological Survey (Open-File Report 99-430 Online version 1.0): Public Review Draft Digital Cartographic Standard for Geologic Map Symbolization (PostScript Implementation). Prepared in cooperation with the Geologic Data Subcommittee of the Federal Geographic Data Committee.

Wikipedia, the free encyclopedia:
! Image editing.
! Image sharpening.
! Photo manipulation.
See especially: ! "Photoshopped".
Category:Photographic techniques.
Computer graphics.

! Sirelious White (2006): Digital Dissection of Radiographs, Using the Early Cretaceous Bird Confuciusornis and Photoshop CS2TM. PDF file, Diss., University of New Orleans.

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This index is compiled and maintained by Klaus-Peter Kelber, Würzburg,
Last updated January 04, 2021

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