Links to microscopy-ralated image processing and acquisition software

Data acquisition

Acquisition & Instrument control. 
CamAcqJ (Grant Harris)
ScanImage (Vijay Iyer, Karel Swoboda): Developed for 2photon microscopy and neurobiology/ patch clamping
Display and Segmentaton
3D Visualisation and analysis (nice rendering) University of Turku & University of Jyväskylä, Finland
Linux/Mac/Windows, VTK + Python based (latest update: 2008‐03‐28)
VisBio  (Curtis Rueden  & Abraham Sorber),
3D Visualisation and analysis (nice rendering). Interfaces with OME.  (latest update: 9 Mar 2009),
V3D (Hanchuan Peng)
Great tools for visualization and segmentation of large (!) datasets. 3D annotation, landmarking, data management,cell segmentation, neuron tracing, deformable registration, and more (latest update 2009‐May‐5)

Image Processing

General Purpose

Voxx: A Volume Rendering Program for 3D Microscopy. Voxx is a voxel‐based (not surface‐based) 3D rendering program which has been optimized for biological microscopy. This software permits researchers to perform real‐time rendering of large microscopy data sets using inexpensive personal computers. We developed it to explore 3D datasets collected on confocal and multiphoton microscopy systems, but it can also render other kinds of data (e.g. CT, MRI, etc.). Old link:; new link:

NIH image (Mac only): NIH Image is a public domain image processing and
analysis program for the Macintosh.
Cell Profiler (Ann Carpenter, MIT)
Versatile 2D processing platform for high throughput screening applications.
IrfanView + IrfanView plugins: Batch conversion (with image processing),
multipage TIF editing, TIFF, AVI, MPEG, DICOM, … (look under “view – Multipage
images”, Extract images from a movie, …
VisBio: VisBio is a biological (3D) visualization tool designed for easy
visualization and analysis of multidimensional image data.
IVE & Priism (Sedat lab, UCSF)
ICY: (Jean-Christophe Olivo Marin et al.)
A powerful general purpose framework form microscopy image processing. Windows based.
View5D: (Rainer Heintzmann, Uni Jena)
Java Applet, ImageJ plugin, Matlab plugin
The program View5D interactively displays of up to 5 dimensional volumetric
datasets. Three orthogonal slicing views, 2D and 3D histograms of intensity (scattergrams),
Basic image processing operations (ratioing, ..), Interactive counting and tagging of
entities, Tracking of 3D movements, Multiplicative display of lifetime or ratio
VTK: For programmers only. The Visualization ToolKit (VTK) is an open source,
freely available software system for 3D computer graphics, image processing,
and visualization. More for expert users, who know how to program. Very
powerful and big community!
BIRN: Selection of various useful tools for image processing and analysis. Mouse
Brain Atlas, 3D Slicer, LONI Pipeline, Functional MRI, …
OME: Open Microscopy Environment
Data management for biological light microscopy. Image‐based analysis of cellular dynamics. Image‐based screens of cellular localization or phenotypes.
OME is a database engine which allows a lab to store all microscopy images along with metadata; keeping track of projects. Some image processing features available.
DIPimage / DIPlib: (Matlab is needed as a platform)
This Matlab toolbox contains a large amount of very useful (often N‐dimensional)
image processing algorithms. DIPimage features its own datatype (dip_image) and
a convenient browser to quickly investigate the results.
Microscopy‐oriented Features are: Automatic Thresholding algorithms, Crosscorrelation‐
based shift determination, Segmentation algorithms (e.g. watershed transform), Noise‐filtering (e.g. anisotropic diffusion with local structure tensors),
Convolution, Measurements of labeled entities (e.g. Major axis direction) …
CudaMat (Rainer Heintzmann)
Using NVidia’s GPUs for fast data crunching in Matlab.
Idea: Make it simple: myImage=cuda(myImage);
Only a subset supported at the moment. Datatypes: single and scomplex
minFunc (Mark Schmidt)
Matlab function for general minimization. Lots of methods implemented.


COSMOS = COSM Open Souce (Chrysanthe Preza)
ImageJ: A public domain Java image processing program inspired by NIH Image for the Macintosh. Windows, Mac OS, Mac OS X and Linux. Plugins ( ) support various microscopy related issues. E.g. time‐stamping, resampling, tracking, … LOOK HERE FIRST
Fiji is just ImageJ:
DeconvolutionLab (Guillaume Schmit, EPFL)
3D_Deconvolution (Pierre Besson, Cédric Vonesch and François Aguet, EPFL)
3D deconvolution package with PSF generation. Only 2^n sized images.
Toolbox for ImageJ with various deconvolution algorithms. Some of them are state of the art wavelet based constraints.
Iterative Deconvolve 3D (Bob Dougherty, OptiNav, Inc.)
Memory intensitve.
DeconvolutionJ (Nick Linnenbrügger)

3D Visualization

Visualize 3D Numpy arrays in Browser
Spimagine is a python package to interactively visualize and process time lapsed volumetric data as generated with modern light sheet microscopes (hence the Spim part).
Python Interface for Fiji/ImageJ (Maybe for View5D implementation?!)
let Python communicate with Java (for image processing)
3D Viewer for volumetric image data
Cell Tracker (Hailin Shen, Univ. of Manchester)
Advanced and useful tool for 2D tracking of cells and features. Uses Snakes. Based
on Matlab. (last update 8 June, 2006)
utrack (Jaquaman, Danuser)
For experts – powerful linking algorithm in Matlab, 3D is possible. Many Matlab toolboxes are needed.
Tracking and Ballon Segmentation, 2D (L. Dupuy)
They also can do tracking but do not show it on the website. Worth asking.
Segmentation pluging can be downloaded:

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