3D Software for Scanning Electron Microscopy

Visit us at: www.m3-sem.com

The 3D Morphometry System M3     splash.bmp

» Download a free demo version (version 3.3)
(user manual, demo pictures and microscope configuration files are included, to be found in the installation subfolders manual, demopictures and res).

System requirements to install the demo version: Windows OS (XP, Vista, Win7, Win10; 32 and 64 bit), OpenOffice 4.x or higher, Java runtime version >1.7
(The installer program automatically checks the requirements and connects to the download site if components are missing on your system).

Demo restrictions: The demo version has full functionality beside the following limitations:
No store/restore function for picturesets and projects, limitation to 2 projects, 3 picturesets per project and 3 measurements per pictureset.

Note! The demo version can be upgraded to the full version. When completing the order form within the demo version (Help menu - Get full version) an order file will be generated which can either be sent via email or saved as text file for later transmitting. Be sure to generate this file on the target PC where the software is intended to be used as M3 won’t run at any other PC! (single PC licence).

3D Morphometry (M3 ) in its current version is now available as state-of-the-art Java based software solution designed for Windows 10 and other operating systems as well. The program easily exchanges data with open office which is freely available and also comes with the package. This means that Mcan now be installed on various platforms such as Windows XP, Windows Vista, Windows 7, Windows 10, Linux and MAC-OS. 32 and 64bit OS versions are supported. 

The software can be installed either on single monitor or dual monitor systems (analogue or digital DVI) or notebooks with no specific hardware requirements.

Scanning electron microscopes (SEMs) are potential tools for morphological research. They have a great resolution and a high depth of focus, which gives SEM micrographs pseudo three-dimensionality. Adversely, the high depth of focus prevents accurate dimensional or spatial measurements of imaged microstructures from either the SEM video-display, printed micrographs or from photo-negatives. Macroscopic objects are viewed close up using binocular vision. Binocular vision is also used in microscopy where stereophotogrammetry and related techniques applying stereopaired images, and a variety of hardware tools calculate the third dimension (z-coordinate) using the parallax.

The method

The method (3D-morphometry, ComServ, Austria) for dimensional and angular measurements of microstructures imaged in the SEM was developed in our lab in 1999. It uses digitized stereopaired images frame-grabbed (slow scan) directly from the SEM’s photo-display, vector equation-based algorithms for calculation of spatial co-ordinates and derived distance- and angular measurements, and offers dynamic data exchange (DDE) together with on-line graphs of frequency distributions of measured variables. Formulas for central perspective depth computation allow the overall error to be less than 1.0%.
The method was now (2008) further improved and the new java based software is suitable to be used with Windows 10 as well. A modern graphical user interface (GUI), new data interfaces (open office) is supported and an improved usability facilitates measurement processes.This technique is currently used to analyze a) the geometry of microvascular trees and b) to determine bifurcation indices and area ratios followed by a calculation of optimality principles which are realized within single arterial bifurcations respectively venous mergings.
This unique package for serious SEM image quantification covers the following tasks:

  • SEM Image Acquisition
  • Processing and Modification of Images
  • 3D Image Generation
  • 3D Morphometry and Quantification
  • Data Exchange (Open Office)

These unique features combined with an easy-to-use Windows interface provides you with effortless analyses. M3 can handle all your 3D image analyzing tasks quickly and accurately. The use of data exchange allows you to fully explore and document your results with in Open Office.

Software specifics 

To view screen shots of the software simply click on the mini previews and navigate between them using the arrows appearing on the left and right border line when draging the mouse over it.

Configuration and convertion: Different configurations for every SEM in use respectively for their different settings of working distances (WD), magnifications, field of views and tilt angles can be stored. A file convertion tool enables to unify the file names of stereopairs so that the corresponding image can be automatically detected and loaded.
File & project administration: The project management allows to overview the status of picturesets (loaded, manipulated, configured, 3D generated and measured) which can also be exported into an open office template. Notes can be taken and emails can be sent in order to inform co-workers about the ongoing project status.
File import: Images can be easily selected from the file chooser (see above). SEM images larger than the desired file size (i.e. 480 vs. 480 pixles) can be croped maintaining the same frame within the corresponding stereopaired images.
Image manipulation: Some image manipulations such as brightness enhancement, sharpening (3×3 kernel filter) as well as image rotation and adjustment of the zoom factor can be applied to the steropairs.
SEM configuration: Every pictureset (stereopair) can either be individually configured depending on the SEM settings used or the default project setting can be applied.
3D image generation: Anaglyphic 3D images can be comfortably generated whereby the false coloured stereopairs might be exactly adopted to the red/green or red/blue filter glasses used (illumination, blue correction). The program also allows to swap the images in case of previous incorrect file storage.
Anaglyphic 3D image: 3D images are intended to provide spatial orientation for the later point setting at the measurements (morphometry). They can be separately zoomed, printed  and saved for external use.

3D morphometry & data export: 3D morphometric measurements on the stereopairs can be performed to examine distances, space angles and volumes calculating the parallax. Every measure can be labeled and indexed, moved and deleted if necessary. Data will be exported into an open office template and frequency distributions are displayed. By later changing of configuration settings (e.g. when inadvertently set) all measurements will automatically be recalculated.

Count, Measure and Analyze your digital 3-D Images quickly and easily:

  • Compute 3D space co-ordinates
  • Measure distances within 3D space
  • Determine volumes of 3D specimen
  • Measure angles within 3D space
  • Use data exchange into OpenOffice spreadsheets

Orders and prizing

Get more information about the program features or place orders please contact us at:  m3_support@comserv.at

Orders: The software will be shipped containing the program CD incl. java bundle, java 3D, openoffice + data templates and sample images. A quick start guide as well as the software manual will be provided as pfd-files. The activation code will be sent via email after payment received.

Prices: € 6.000,- incl. VAT (University discount of 20% can be granted)

Note! The demo version can be upgraded to the full version. When completing the order form within the demo version (Help menu - Get full version) an order file will be generated which can either be sent via email or saved as text file for later transmitting. Be sure to generate this file on the target PC where the software is intended to be used as M3 won’t run at any other PC! (single PC licence).


[1] Minnich, B., Leeb, H., Bernroider E.W.N. and Lametschwandtner, A. (1999) Three-dimensional morphometry in scanning electron microscopy: A technique for accurate dimensional and angular measurements of microstructures using stereo paired digitized images and digital image analysis, Journal of Microscopy, 195 (1): 23-33. 

[2] Minnich, B. and Lametschwandtner, A. (2000) Lengths measurements in microvascular corrosion castings - 2D versus 3D morphometry, SCANNING, 22 (3): 173-177.

[3] Minnich, B., Krautgartner W.D., Leeb, H., Bernroider, E.W.N. and Lametschwandtner A. (2002) Quantification of Complex Three-dimensional Microstructuresby Stereo paired Scanning Electron Imaging and PC-based 3D-Morphometry, in FORMATEX, Science, Technology and Education of Microscopy: An Overview, Vol.II: 706-711. ISBN: 84-607-6699-3.

[4] Kachlik, D., Baca, V., Stingl, J., Sosna, B., Lametschwandtner, A., Minnich, B. and Setina, M. (2007) Architectonic Arrangement of the Vasa Vasorum of the Human Great Saphenous Vein. Journal of Vascular Research, DOI: 10.1159/000099142; Vol.44: 157-166.

[5] Kachlik, D., Stingl, J., Sosna, B., Starka, Z., Lametschwandtner, A., Minnich, B. and Fara, P. (2008) Morphological features of vasa vasorum in pathologically changed human great saphenous vein and its tributaries. VASA, DOI: 10.1024/0301-1526.37.2.127, 37(2): 127-136.

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Tel.: 0664-84 82 302
Fax.: 06221-20177

E-Mail: office@comserv.at


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