Software Listing: Microscopy

The Generalized Video Microscopy Analysis application is built as a small software that can analyze the motion of cells that are captured with the help of fluorescent video microscopy.

Being developed in the Java programming language, Generalized Video Microscopy Analysis is a tool that can run on multiple platforms.


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  • Platform: WinOther

A powerful software for analysis of different kinds of microscopic images. Mainly oriented for the scanning probe microscopy 3D images processing and analysis, but can be also used for optical and electron microscopy images. Between its features are powerful 3D representation, with ability to record movies, clipboard integration, USB cameras support, Fourier analysis, pattern recognition functions. You will be able to easily measure spatial dimensions of any object, calculate the roughness parameters or build histograms. A special attention is payed to the processing of the force curves - calculation of separation curves, WLC model approximation, calculation of statistics for multiple curves.

  • Platform: WinOther

Computer Controlled Optical Microscopy is a package to enable camera equipped microscopes to generate multi-modal time-lapse image sequencesof 3D volumes. This is achieved by periodically changing optical settings, xyz positions and acquiring images..

  • Platform: Linux, Unix

XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es.

  • Platform: Linux, Unix, WinOther

A modular, database-backed system for 5 dimensional (5D) analytical biological microscopy and cell-based screening. Please note - we have moved. Please come visit us and download from our new site at http://cvs.openmicroscopy.org.uk
Open Microscopy Environment License - GNU General Public License (GPL).

  • Platform: WinOther

LabVIEW based X Scanning Microscopy Project.
LabVIEW based X Scanning Microscopy License - GNU General Public License (GPL).

  • Publisher: Lxsm
  • Date:
  • Platform: WinOther
  • JRobust
  • License: Freeware
  • Price: 0.00
  • Rating

JRobust will provide you with a user-friendly application designed for Atomic Force Microscopy data analysis.

JRobust can analyze AFM images and extract mechanical properties from force curves. It can create map and image histograms and generate detailed statistics.



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  • Platform: Win7 x64

GoFigure2 is a handy, easy to use tool specially designed to help you visualize, process and analyze multidimensional microscopy data.

Users can visualize, segment and track cells through time, detect cell-division and ultimately generate lineages.
for WindowsXP, Vista, 7

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  • Platform: Windows 7, WinOther, WinVista

High Performance 3D-4D imaging software for a better insight to your science. Volocity is the universal solution for 3D analysis of fluorescence microscopy images. A collection of high performance 3D imaging software products, Volocity lets you turn images into understanding, relate cellular structure to function and deliver quantitative measurements for publication. * Acquisition * Visualization * Quantitation * Restoration Volocity Acquisition Volocity® Acquisition is the ultimate solution for high speed, 3D image capture. New 64-bit acquisition boosts the maximum size of a single time-point that can be acquired and is only limited by your disk space.

  • Publisher: PerkinElmer
  • Date: 09-10-2012
  • Size: 187392 KB
  • Platform: WinOther

High Performance 3D-4D imaging software for a better insight to your science. Volocity is the universal solution for 3D analysis of fluorescence microscopy images. A collection of high performance 3D imaging software products, Volocity lets you turn images into understanding, relate cellular structure to function and deliver quantitative measurements for publication. * Acquisition * Visualization * Quantitation * Restoration Volocity Acquisition Volocity® Acquisition is the ultimate solution for high speed, 3D image capture. New 64-bit acquisition boosts the maximum size of a single time-point that can be acquired and is only limited by your disk space.

  • Publisher: PerkinElmer
  • Date: 01-11-2012
  • Size: 187392 KB
  • Platform: WinOther

This toolkit allows complete control of a microscopy setup from Labview, Matlab, Scilab, Python, .Net, VB, IgorPro, Mathematica and more. Included is a standalone program for image acquisition and scripting control of a scientific microscope..

  • Platform: WinOther
  • Camscope
  • License: Freeware
  • Price: 0.00
  • Rating

Camscope is a multi-threaded program for acquiring and quantitatively analyzing images from an IIDC-compliant FireWire camera. It provides an integrated environment for performing quantitative video microscopy for teaching laboratories..

  • Platform: Linux, Unix
  • GXSM
  • License: Freeware
  • Price: 0.00
  • Rating

GXSM -- Gnome X Scanning Microscopy: A multi-channel image and vector-probe data acquisition and visualization system designed for SPM techniques (STM,AFM..), but also SPA-LEED. A plug-in interface allows any user add-on data-processing and special hardware and instrument support. Based on several hardware options it supports a commercially available DSP hardware and provided also Open Source Code for all the low level signal processing tasks and instrument controls in a most flexible and adaptable manner. All latest software is available via CVS only or Live Demo/Install CD: http://www.ventiotec.

  • Platform: Linux, Mac OS X, Unix, WinOther
  • PHLIP
  • License: Freeware
  • Price: 0.00
  • Rating

PHLIP is a MATLAB centric academic software application for quantification of biofilm structure from confocal laser scanning microscopy (CLSM) data, intended for automated processing and statistical analysis of large data sets produced by CLSM..

  • Platform: WinOther

A web-driven database for 2-D and 3-D images, specifically designed for (confocal) microscopy units, but applicable wherever groups of users collaborate with images..

  • Platform: Linux, Unix

This is the software to analysis the atomic force microscopy images. Average feature size and area can be calculated using this software. Steps to follow - 1 - First remove any additional part of the image not included in the scan area using software like paint etc. 2 - Browse the image and load it into the software. 3 - Move the first (top) slide bar, you will observe the boundary appearing near the patches (AFM features). Select the desired patches. 4 - Remove the unwanted small patches by moving the second slidebar. 5 - Information like number of patches, average diameter and area will be updated in real time.

  • Platform: Matlab, Scripts

SimPartCohImg uses 'sum over the source' algorithm to compute the images produced by partially coherent (i.e., non-fluorescent) imaging systems such as phase microscopes and optical lithography systems. This is perhaps the first freely available code for this purpose. Total image is the sum of the images produced due to individual condenser points. I have placed special emphasis on ensuring accuracy of the computation. The computed images match very well with analytical results (for cases where analyical expressions can be derived). Please refer to two accompanying published test benches : One test bench verifies the accuracy of computation and the other illustrates the usage of the code for computing microscopy images.

  • Platform: Matlab, Scripts

This directory contains m-functions for reading and writing files used in electron microscopy and 3D reconstruction. The file formats those used by the IMAGIC software package (Image Science GmbH; EMAN and Frealign are public-domain programs that also use this format), the MRC program library, and the Digital Micrograph (Gatan, Inc.) file format. These functions were written on what published information we could find, and work for our limited purposes; they are not supported by the software authors at all. The functions generally assume that little-endian files are being read by a little-endian machine.

  • Platform: Matlab, Scripts

SPIDER is a free image processing system for electron microscopy. It is used for three-dimensional reconstruction of single particle macromolecules, multivariate statistical classification, and electron tomography. See the extensive documentation and many available techniques at www.wadsworth.org/spider_doc/spider/docs/master.html SPIDER has its own binary format for images and volumes. The SPIDER M-file collection lets users read SPIDER images, volumes, image stacks, and textual document files directly into Matlab data types for processing and visualization..

  • Publisher: Bill Baxter
  • Date: 10-04-2013
  • Size: 1720 KB
  • Platform: Matlab, Scripts

An automated data analysis method for atmospheric particles using scanning transmission X-ray microscopy coupled with near edge X-ray fine structure spectroscopy (STXM/NEXAFS). This method is applied to complex internally mixed submicron particles containing organic and inorganic material. Several algorithms were developed to exploit NEXAFS spectral features in the energy range from 278-320 eV for quantitative mapping of the spatial distribution of elemental carbon, organic carbon, potassium, and non-carbonaceous elements in particles of mixed composition. This energy range encompasses the carbon K-edge and potassium L2 and L3 edges.

  • Publisher: Ryan Moffet
  • Date: 13-04-2013
  • Size: 1229 KB
  • Platform: Matlab, Scripts

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