Free Softwares

Data acquisition

μManager is a software package for control of automated microscopes. Microscope control and Image capture.

Developed for 2P microscopy and neurobiology/ patch clamping

Display and Segmentation

BioimageXD   3D visualisation and analysis. University of Truku and University of Jyväskylä, Finland. Linux/Mac/Windows, VTK + Python based 

3D visualisation and analysis. Interface with OME 

 3D visualisation and analysis for "huge" data (several Go, acquired with a SPIM for example).

Need to download the TerFly plugin for Vaa3D

Image Processing

  =COSM Open Source               
ImageJ (Win/Mac/Linux) Image quantification and analysis with a very large number of plug-ins. Many online tutorials and a very active user community.
Fiji (Win/Mac/Linux) Based on ImageJ but organized differently and with a large number of selected high-quality plug-ins preinstalled.
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.
Cell Profiler (Win/Mac) High-throughput image analysis pipelining. Can utilize ImageJ functions.
IrfanView   Batch cnversion (with image processing), multipage TIF editing, TIFF, AVI, MPEG, DICOM, ... (look under "view- Multipage images", Extract images from a movie,....
VisBio   A biological (3D) visualisation tool designed for easy visualisation and analaysis of multidimensional image data.
IVE & Priism   Priism is a collection of tools for processing, analyzing, and visualizing multidimensional imagery with a focus on 3D wide-field optical microscopy and EM tomography. IVE (Image Visualization environment) is the core set of software libraries that are the foundation for the tools in Priism. The two are available as a package for x86 and x86_64 Linux and Mac OS X for Intel.
Icy (Win/Mac) A new image quantification and analysis package with advanced 3D visualization via the VTK libraries. Has a plug-in architecture and can use some ImageJ plug-ins.
 Neuron Studio  (Win) This program is designed to allow reconstruction of neuronal structures from confocal and multi-photon images. It is a self-contained software package that is free, easy to use, and available for 64-bit computers. NeuronStudio provides tools for manual, semi-manual, and automatic tracing of the dendritic arbor as well as manual and automatic detection and classification of dendritic spines. In addition, advanced 2D and 3D visualization techniques facilitate the verification of the reconstruction, as well as allowing accurate manual editing. The output of the program is compatible with standard compartment modeling and morphometric software applications. 


Cell tracker   Advanced and useful tool for 2D tracking of cells and features. Uses Snakes . Based on Matlab 
View5D   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, tracking of 3D movements, multiplicative display of lifetime or ration images. 


(Win/Mac/Linux) Client–server storage, visualization, and analysis of microscopy imaging. Includes a metadata model to describe imaging experiments. ImageJ client plug-in available.
minFunc   Matlab function for general minmization. Lots of methods implemented.