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  Petr Schauer

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Microscopy Courses & Software

You can find on this page:





  • AFMHelp.com The site is designed to offer help with atomic force microscopy (AFM).

  • Cell Structure and Function Online Learning Center of McGraw-Hill textbooks.

  • Diffraction An introductional online course from Matter Online.

  • Gamma Ray Spectrometry GammaSpec.org - an interactive web site for high resolution gamma spectrometry, based on the well established radiometrics course at the University of Liverpool.

  • JEOL Tutorials Scanning Electron Microscopes, Mass Spectrometers, ..

  • Lehigh Microscopy School SEM, X-ray Analysis, AEM, AFM.

  • Micro-Scope An online reference guide to microscopy.

  • TEM Basics An introductional online course in Transmission Electron Microscopy from Matter Online.

  • How Light Works by Craig Freudenrich - Introduction to How Light Works, Ways of Thinking About Light, What is Light, Producing a Photon, Making Colors, When Light Hits an Object, Rainbows in Soap Bubbles, Lots More Information, ..

  • Introduction to Microscopy You will get information about the light microscope and about the subjects you can study through the microscope.

  • Molecular Expressions Microscopy Primer This site reviews basic and advanced topics and concepts in optics, light, color, optical microscopy, digital imaging, photomicrography, fluorescence and features over 200 interactive Java tutorials.

  • Nikon's MicroscopyU An educational forum for all aspects of optical microscopy, digital imaging, and photomicrography. The website is providing the latest state-of-the-art information in microscope optics and imaging technology including specialized techniques such as fluorescence, differential interference contrast (DIC), phase contrast, reflected light microscopy, and microscopy of living cells.

  • Optics for Kids Science and Engineering by Bruce Irving, Optical Research Associates

  • Protrain Electron Microscopy Courses Maintenance, SEM, TEM and EDX

  • SVI Wiki 3D microscopy, deconvolution, visualization and analysis.



  • Advanced DataBase Systems, Denver, (CO, USA) Powerful image databases focused on imaging. XML/Oracle/SQL technology allows images and data to be captured through the web. Integration of ImageJ from NIH adds to our flexibility. Desktop applications are available for all Windows platforms. Image adjustment, measuring, printing, report generation, email are a few of the tools supplied with our applications.

  • ANL Software Library Microscopy & Microanalysis Software Libraries (USA)

  • Emispec Systems ES Vision is capable of interfacing with most commercially available detectors, including: EDX and EELS spectrometers, slow-scan CCD cameras, video cameras and SE/BSE/BF/DF/HAADF scanning detectors. These detectors are all controlled through one Base Data Acquisition computer. By being able to interface with and control all of these detectors simultaneously, never before possible experiments such as simultaneous EDX and EELS mapping are now routine.

  • EMS OnLine

  • FemtoScan Online Software Moscow, (Russian Federation) FemtoScan Online software is designed primarily to analyze SPM images. It can also be used for electron and optical microscopy data analysis, and for processing of images in standard formats.

  • Fiji Fiji is an image processing package. It can be described as a distribution of ImageJ (and soon ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. The main focus of Fiji is to assist research in life sciences. Fiji is easy to install and has an automatic update function, bundles a lot of plugins and offers comprehensive documentation. Fiji is an open source project with access to the source code of all internals, libraries and plugins.

  • FreeSFP Hilversum, (The Netherlands) Freeware! FreeSFP allows high speed and high quality visualization of volume data acquired with 3D microscopes or medical equipment like MRI or CT scanners. FreeSFP consists of a fast renderer linked to a high quality ray tracing renderer. The fast renderer creates a thumbnail on the fly with which you can determine the image as you would like it to be rendered in full. After that, you can render the data in a big image.

  • HeliconFocus Software Kharkiv, (Ukraine) Program creates one sharp image of superb quality from several partially sharp images.

  • Huygens Essential Hilversum, (The Netherlands) Using this software you can restore images with great ease as its wizard-driven user interface guides you though the deconvolution of your images step by step. Just like the Professional edition, it can process images from many current optical microscopes, including widefield, confocal, Nipkow Disk, multiple-photon, and 4Pi microscopes. Powerful and fast renderers produce different representations of your data, not needing any special graphic card.

  • Huygens Scripting Hilversum, (The Netherlands) This software enables you to process very easily large quantities of datasets automatically by using a number of preformatted scripts which can easily be adjusted to those particular datasets. Combined with powerful hardware this is ideal for imaging centers that need automation due to a high throughput of data.

  • ImageJ Public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.1 or later virtual machine. Downloadable distributions are available for Windows, Mac OS, Mac OS X and Linux.

  • Lispix is public domain image analysis program for Windows, written and maintained by David Bright. It includes basic image processing functions, and also a collection of special purpose research tools for electron microscopy and spectral imaging. It is useful for processing and analyzing images, and stacks of images or data cubes.

  • MS MacroSystem - 3D visualization software Maarn, (The Netherlands) 3D surface software for interactive analysis and measurement of the SPM/AFM data: Applications and ActiveX components

  • Multiple Image Tool Rostock, (Mecklenburg-Vorpommern, Germany) Software for efficient work with very large and highly multi-dimensional image data in an intuitive and natural manner. The Browser is capable of handling image data of any size containing up to four dimensions with Data annotation and 3D-Visualization.

  • Nanosurf demo software Liestal, (Switzerland) Software contains an STM/AFM microscope simulation mode that allows users to get an idea of what it means to operate an AFM or STM. The simulation mode mimics most features of the full version of Nanosurf control software and contains mathematical functions that generates “realistic” sample images that can be zoomed into, moved, measured, analyzed, etc.

  • ORION for Windows Charleroi, (Belgium) High resolution grabbing software for SEMs. A lot of useful functions are easily available: zoom, distance measurements, image extraction, text inclusions,...

  • Remote Microscope Free software for controlling a fully automated semiconductor inspection microscope, letting designers view their wafers over the Internet.

  • Saturn active drive for SEMs Charleroi, (Belgium) SATURN is a very flexible SEM active drive system, designed for interfacing nearly any type of SEM. The Saturn board is placed in the SEM and does not need any external power supply. The connection to the computer is very simple and requires only a serial COM port.

  • SIMAGIS, New concept of image processing tables makes image processing and analysis as easy and effective as adding numbers in a spreadsheet.

  • SIMION Ion and Electron Optics Program.

  • Total Resolution, Berkeley, (CA, USA) Specializing in scientific software for use in electron microscopy & crystallography.

  • TrueGage North Huntingdon, (PA, USA) - Microscopy Image Visualization and Analysis. TrueGage is a provider of software solutions for micro and nano-surface metrology for use in research laboratory, industrial, and production environments.

  • VayTek Image (TM) Image processing and data acquisition software. It allows scientists to capture images in real time from their microscope and process the images to bring out the relevant features. This free download of VayTek Image provides software that can only use existing images to perform its functions. VayTek Image is designed to capture images from various digital cameras.

  • VayTek VoxBlast Fully featured 3-D digital imaging application for science, engineering and medicine. It offers 3-D Measurement, 3-D Volume Visualization, and 3-D Rendering.



Page updated on: September 19, 2013, 14:16
Page compiled by: Petr Schauer, Petr@ISIBrno.Cz


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