Palaeobotanical Tools /
Focus stacking (Photography, Extended Depth of Field)
Preparation and Conservation
Palynological Preparation Techniques
Cellulose Peel Technique
Photography and Scanning
Digital Cameras on the Microscope
High Dynamic Range Imaging (HDR)
Transmission Electron Microscopy (TEM)
Microtomography (CT Scanning, XTM) including Synchrotron X-ray Tomographic Microscopy (SRXTM)
Writing, Translating and Drawing
! Panorama Creation and Stitching Tools@
! Scientific Drawing@
Glossaries, Dictionaries and Encyclopedias: Microscopy@
! A. Agarwala et al.: Interactive Digital Photomontage. In PDF. See also here.
! ALE 0.8.8.1 (David Hilvert). ALE is a freeware image-processing program used for tasks such as image mosaicking, super-resolution, deblurring, noise reduction, etc.
! Peter Bargh, YouTube: Focus Stacking - a macro photography technique. The use of free Combine ZM software or Helicon Focus software.
R.S. Barclay et al. (2013): New methods reveal oldest known fossil epiphyllous moss: Bryiidites utahensis gen. et sp. nov.(Bryidae). In PDF, American Journal of Botany, 100: 2450-2457.
! A. Bercovici et al. (2009): Improving depth of field resolution for palynological photomicrography. PDF file, Palaeontologia Electronica, Vol. 12.
V. Blagoderov et al. (2012): No specimen left behind: industrial scale digitization of natural history collections. In PDF, Zookeys, 2012, (209): 133-146.
Bradley, A.P., Wildermoth, M. and Mills, P. (2005): Virtual Microscopy with Extended Depth of Field. Abstract, Digital Image Computing: Techniques and Applications (DICTA'05), Cairns, Australia.
J. Brecko et al. (2014):
Comparing commercial top-end set-ups with a semi-automatic low budget approach.
A possible solution for mass digitization of type specimens. In PDF,
ZooKeys, 464: 1-23. With a comparison of different focus stacking
software packages (PDF page 19). Excellent!
See also here.
Matt Brett, Digital Photography School, Canada: An Introduction to Focus Stacking.
Cambridge in Colour: This is an online learning environment where photographers can come to improve their skills. Focus Stacking.
Canon Digital Photography Forums: Which Focus Stacking Software?
Cyclopedia.net: Focus stacking. Search results (in German).
Dennis Goulet Photography: Focus Stacking - Part 3, What Works, What Doesn´t.
! dmoz open directory project: Arts > Photography > Techniques and Styles.
H. Failmezger et al. (2013): Semi-automated 3D Leaf Reconstruction and Analysis of Trichome Patterning from Light Microscopic Images. In PDF, see also here.
flickr: Macro Viewers / Discussion: Focus stacking Tutorial. Using the freeware programme combinez5 and links to other tutorials. See also here.
FocOz: FocOz Software. This program is comparing different frames, selecting image elements of high definition from them all and rejects whatever is blurred.
Daniel Glasner et al.: Super-Resolution From a Single Image.
P. Gould (2012): Focus Stacking: How to Simultaneously Focus on Several Photographs Using Adobe Photoshop CS4. Abstract, Identification Canada.
Stefan Gross, Traumflieger: Photoshop-Workshops, Mehr Schärfentiefe mit Photoshop. The Photoshop procedure, a tutorial (in German).
Alan Hadley, U.K.:
CombineZ Movie CZM).
The purpose of this free program is to increase depth of focus by combining pictures, but
each picture should be in focus at a different depth into the scene. The program is especially
useful to microscope users (e.g. palynomorphs) 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 the former CombineZ5. Still available:
CombineZ5. It works with older versions of windows, but is not maintained anymore. See also:
Yahoo Group combinez,
Forum discussions (Digital Grin), or
Tutorials are here (flickr), and there (Brian Valentine).
John Hart, Program in Atmospheric and Oceanic Sciences, University of Colorado: IMAGE STACKS AND AUTOMONTAGE RESULTS Using the software AutoMontage (Synoptics Ltd.).
J.T. Haug et al. (2011): Autofluorescence imaging, an excellent tool for comparative morphology. In PDF, Journal of Microscopy.
Helicon Soft Ltd.,
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.
See also Video Tutorials.
! John Hollenberg, Digital Outback Photo: Workflow Technique 072. Review of Helicon Focus and CombineZ5 software. Excellent!
! Neal Immega,
Houston Gem and Mineral Society:
how2doit Articles. Go to:
Extended Focus in Macro Photography (PDF file). A CombineZ5 tutorial. See also here.
Infognition: What is super-resolution?
! Johan J. Ingles-Le Nobel, United Kingdom: Extreme Macro Photography. See especially: Macro Stacking.
O. Jaurich (?): Mikroskopie und mikroskopische Bildverarbeitung, Nachbearbeitung der aufgenommenen Bilder. About CombineZ5 (in German).
Biomedical Imaging Group, EPFL, Lausanne, Switzerland: Extended Depth of Field. Extended depth of field is an image-processing method e.g. to obtain in focus microscopic images of 3D objects. Free and easy-to-use focus stacking software.
Rik Littlefield, Richland, WA:
An Introduction to
Extended Depth of Field Digital Photography
(from News of the Lepidopterists' Society, Summer 2005) and
Extended Depth of Field Photography of Insects. The software used here was CombineZ5. See also: Extended Depth-Of-Field Using Panorama Tools.
! 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.
TawbaWare is home to software, photographs, and writings. Go to:
TuFuse Pro. Graphical Exposure and Focus Blending Software.
Makrotreff: Focus Stacking leicht gemacht. In German.
Media Cybernetics Inc.: Image-Pro Plus. The Extended Depth of Field function in Image-Pro Plus provides you with the ability to display a stack of images as a composite, building in effect a three dimensional image.
National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland (program developed by an employee of the Federal Government in the course of his official duties): ImageJ. ImageJ is a public domain Java image processing program. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.4 or later virtual machine. It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images (including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw"). ImageJ supports "stacks" and standard image processing functions such as contrast manipulation, sharpening, smoothing, edge detection and median filtering. It can calculate area and pixel value statistics of user-defined selections, measure distances and angles and it can create density histograms and line profile plots.
! Optronics: Rincon. An image measurement and processing software. Rincon can combine a stack of images captured at different levels of focus and combine them into a single in-focus image.
Pentaxforums.com: Macro photo stacking software comparison.
PhotoAcute, Austin, Texas, USA: Superresolution FAQ.
! PICOLAY (from PICture OverLAY, by Heribert Cypionka, Institut für Chemie und Biologie des Meeres, Universität Oldenburg, Germany). This is a freeware program for Windows computers designed for the extraction of improved images from digital picture series. Excellent!
! J. Piper (2010), go to PDF page 190: Software-Based Stacking Techniques to Enhance Depth of Field and Dynamic Range in Digital Photomicrography (PDF file). In: T.D. Hewitson, I.A. Darby (eds.), Histology Protocols, Methods in Molecular Biology 611.
Reindeer Graphics, Asheville, NC: Optipix software.
Ruedi Rottermann et al. (2010): How Sharp Images Are Formed - Depth of Field in Microscopy. About the Multifocus module of the Leica Application Suite (LAS).
Saphicon: AllFocus. The AllFocus software aligns images in the Z-stack by shifting and scaling them and creates a composite image by choosing pixels from the best-focused plane.
H.A. Schmid, Pilze Forum: Coolpix-Lupenmakro/CombineZ5 (Anleitung). About CombineZ5 (in German).
! Stefan Schorn, Mineralienatlas, Germany: Digitale Mehrebenen-Fotografie (DMF) / Digitale Fokuserweiterung. A tutorial, including a list of further focus stacking software programs (in German). See also: CombineZ5 / CombineZM.
SCM Altivid, Berlin: Mikroskopkamera (in German). A low-cost camera with extended depth of field.
! Synoptics Ltd., Frederick, MD: AUTO-MONTAGE FOR PERFECTLY FOCUSED 3D IMAGES, and Free downloadable demonstration software. Auto-Montage enables the processing of a series of images producing a high quality focused image. Lots of examples are listed here.
TAXONOMIC TOOLS BY COMPUTER 2 (TTBC2)
! Brian Valentine: Wonderful Photos: How to Increase your Depth of Field by Focus Stacking. A tutorial on using the freeware CombineZM (by Alan Hadley, U.K.).
Berthold Weber, Weiden:
! Digitale Mehrebenenfotografie.
Wikipedia, the free encyclopedia:
! Focus stacking.
Category:Free photo software.
Kurt Wirz, Switzerland:
A gallery of beautiful focus stacking images. See especially:
! Making of
Zerene Stacker (by Zerene Systems, LLC.,
is a "focus stacking" program designed specifically for challenging
macro subjects and discerning photographers.
The new programme Zerene Stacker is available for a free trial period.
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