Free open source software for analysis and visualization of multidimensional biomedical images. BioImage XD is a collaborative open source free software project, designed and developed by microscopists, cell biologists and programmers from the Universities of Jyväskylä and Turku in Finland, Max Planck Institute CBG, Dresden, Germany and collaborators worldwide.

Development environment for medical image processing and visualization developed and used by the MeVis Research GmbH in Bremen – Germany. MeVis Research develops scientific methods and software for computer assistance in medicine in general and radiology in particular, including computer aided diagnosis, therapy planning and monitoring, and computer aided teaching and training. One of the main goals of MeVis Research is to achieve practically useful solutions to clinically relevant problems, incorporating state of the art knowledge from the natural sciences, mathematics and computer science. The MeVisLab SDK Unregistered license allows to use the MeVisLab SDK with restricted functionality for non-commercial purposes without obtaining a separate license file.

Free and Open Source image processing software dedicated to DICOM images (“.dcm” / “.DCM” extension) produced by medical equipment (MRI, CT, PET, PET-CT, …) and confocal microscopy (LSM and BioRAD-PIC format) but can also read many other file formats: TIFF (8,16, 32 bits), JPEG, PDF, AVI, MPEG and Quicktime. OsiriX has been specifically designed for navigation and visualization of multimodality and multidimensional images: 2D, 3D, 4D and 5D Viewer.

VolView is an intuitive, interactive system for volume visualization that allows researchers to quickly explore complex 3D medical or scientific images. Users can easily generate informative images to include in reports and presentations. Data exploration and analysis is enhanced through tools such as filtering, contours, measurements, histograms, and annotation.

Free of charge version of the lite version of the confocal software LAS AF (Leica Application Suite). It allows you to read and export the .lif files generated by the confocal software. With this program you will be able to work on your .lif files acquired with all Leica acquiring systems.

‘Lite’ version of the Leica Confocal Software. It is limited in its application but it does allow you to view your image files, make simple volume projections and animations, and perform basic image processing and analysis.

Light version of Improvision Volocity software. Can open/export Volocity libraries.

This free software package allows to view Nikon confocal images in the native ics/ids format.

Freeware version of the Huygens deconvolution software. FreeSFP is a free of charge volume renderer that enables you to explore 3D digital images and Simulated Fluorenscence Process.

Light version of Zeiss Axiovision 4.5 software can open .zvi files, owner Zeiss file format.

Light version of Zeiss LSM510 software. Can open multi-dimensional image from several file types (including Zeiss LSM), visualize/export them and includes basic analysis tools.

Free of charge version of Zeiss Confocal Software Package ZEN. ZEN LE can open and compare up to 19 different image file formats including multidimensional LSM and ZVI -images, edit (display adjustament, unmix, filtering), measure, annotate, and export file formats including .mov and .avi.

Freeware tool for the semi-manual or semi-automatic reconstruction of neurons for single images or image stacks. It is being developed primarily by Darren Myatt of the University of Reading – UK – It is completely free to use for non-commercial purposes, such as academic research.

Free software developed at Yale University – USA – for empirically-based simulations of neurons and networks of neurons.

CellProfiler cell image analysis software is designed for biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

CellTracker is a free software for image browsing, processing and cell tracking. Using this software, you can track your targets in living cell imaging. It supports multiple export formats, including TIFF image, AVI video, spreadsheet and XML files. It’s designed for biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

Nice software for volume rendering provides facility to animate transfer functions, animate volumetric time series, animate sub-volumes, etc.

Image Surfer is a open-source, user-friendly and intuitive interactive software package for volume visualization and data analysis that enables researchers to explore complex 3D confocal images. ImageSurfer incorporates traditional visualization tools such as maximum intensity projection, direct volume rendering, and a specialized isosurface rendering, as well as advanced tools to analyze and quantify relationships between multi-channel confocal images. Detailed analysis can be carried out using a 2D slice extractor combined with display of height fields; data can be extracted along a user-defined curve and exported to standard statistical softwares.

ImageJ is a public domain, Java-based image processing program developed at the National Institutes of Health (NIH). ImageJ was designed with an open architecture that provides extensibility via Java plugins and recordable macros. Custom acquisition, analysis and processing plugins can be developed. User-written plugins make it possible to solve many image processing and analysis problems. Very popular, powerful, free, with many plugins, image processing software compatible operating system.

UTHSCSA ImageTool is a free image processing and analysis program. It was developed in the Department of Dental Diagnostic Science at The University of Texas Health Science Center, San Antonio, Texas – USA. The program was developed by C. Donald Wilcox, S. Brent Dove, W. Doss McDavid and David B. Greer. ImageTool was designed with an open architecture that provides extensiblity via a variety of plug-ins. It was written using Borland’s C++ version 5.0.2 and the source code for the executable is also available free of charge.

ImageTrak is an image analysis program designed for converting, viewing, and quantitatively analyzing scientific image data. Either single images, 3D image stacks or 4D data (3D vs. time) can be processed. Although ImageTrak was specifically designed for fluorescence microscopy, virtually any type of TIFF image can be imported, examined, and analyzed (eg. Western blots).

Free software developed by Christof Schwiening (pH Lab, University of Cambridge – UK). LSM toolbox allows to browse Zeiss, Leica and other image data, allows complex, non-continuous regions of interest (as many as you like) to be plotted as either absolute intensity of background subtracted F/F0. You can also filter images with a variety of matrices and track and fill moving objects. The program is very small (~700KB) and run on a 486 machine with 64MB of RAM and still analyze a 10GB file.

MIATool (The Microscopy Image Analysis Tool) is a Matlab addon for microscopy. Created specifically for analyzing large sets of images. Besides image viewing and editing, MIATool supports organization of data on disk and some advanced image processing capabilities. Written in MATLAB using the object-oriented methodology, MIATool achieves efficient usage of memory and disk space through the use of image pointers and MATLAB objects. To obtain MIATool, must be fill out and submit the MIATool Information Form (webform) to request a copy of the MIATool Software.

Designed with the need to visualize large data sets in mind. The goals of the ParaView project include the develop an open-source, multi-platform visualization application, support distributed computation models to process large data sets, create an open, flexible, and intuitive user interface and develop an extensible architecture based on open standards.

Software developed by Prof. Fiala and his Reconstruct Users Group at Boston University – USA -, allows application for montaging, aligning, tracing, measuring, and reconstructing objects from serial section images, both from EM and OM images.

Sinema is Single Particle Tracking software, used for quantum dot labeling and diffusion measurements developed at Optics & Biology Group – Laboratoire Kastler Brossel, Département de Physique de l’Ecole normale supérieure, Paris f France. Sinema is an easy-to-use tool to detect and track fluorescent particles in time-lapse image sequences.

Software developed at the CNIC (Computational Neurobiology and Imaging Center, Mount Sinai School of Medicine, New York – USA) allows multiple stacks of tiled optical sections obtained to be interactively tiled in 3D and integrated into a single volumetric dataset.

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. Developed 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.).

Blender is the free open source 3D content creation suite under the GNU General Public License. It’s a very powerful program for graphics animation and video production. It can be used for modeling, UV unwrapping, texturing, rigging, skinning, animating, rendering, particle and other simulating, non-linear editing, compositing, and creating interactive 3D applications.

IrfanView is a very fast, small, compact graphic viewer. It was the first Windows graphic viewer WORLDWIDE with Multiple (animated) GIF support, multipage TIF support, multiple ICO support. It does not have extensive image creation and painting capabilities like Adobe Photoshop or GNU’s GIMP. Rather, IrfanView is designed to be a lightweight viewer/player which is noted for its speed, ease of use, and ability to handle a wide variety of graphic file formats; good support for batch operations. Please note, many Photoshop compatible plugins work with Irfanview as well.

PhotoShop is too expensive or are you bored by then? The GIMP is the GNU Image Manipulation Program. It is a freely distributed piece of software for such tasks as photo retouching, image composition and image authoring.

VectorMagic is a powerful, highly interactive online tool for precision vectorization (tracing) of raster (bitmap) images. It allows the user to refine the tracing operations and to verify in great details the results. VectorMagic proves to be much better than both Adobe Live Trace (Illustrator CS2) and Corel PowerTrace (CorelDraw X3). File formats supported (max size: 5 MB):

• Input: JPG, GIF, PNG, BMP, TIFF
• Output: PDF, EPS, SVG, PNG

Freeware and Open Source video player. It started as a student project at the French École Centrale de Paris but is now a worldwide project released under the GNU General Public License.

Freeware and easy software to process and convert or compress your movies, also from old-movies format.

Nices and useful small softwares available for Mac. About many categories, biology, physics, optics, visualization, image management.

• Open Modeller DesktopDownload
• BALLViewDownload
• PhyloCoco Download
• CLC Free WorkbenchDownload
• Molecular WorkbenchDownload
• miXscope Download
• QXScope Download
• MedINRIA Download
• ChemoDoseMacX Download
• Geneious Download
• Plot Download
• DicomCMDownload
• LabAssistantDownload
• Serial Cloner Download
• A/G BLASTDownload
• LensForge Download
• Raw Photo ProcessorDownload
• LiveQuartz Download
• ConverTable UnitsDownload
• CoherentOpticsDownload
• mMass Download
• BlastViewerDownload

µManager is an Open Source software package for imaging and control of automated microscopes on multiple platforms. Together with ImageJ, µManager provides a comprehensive imaging solution – comparable to commercially available ones.

Very useful and interesting page about absorption, fluorescence, transmission and reflectance spectral data. PubSpectra and Fluorescent Spectra: An Interactive Exploratory Database (“Fluorescent Spectra Graphing Site”) have been developed in a collaboration between George McNamara and Carl Boswell. Authors encourage researchers and spectral companies to repost the data files on their own web sites.

CBL (Computational Biophysics Lab) at Institute of Computational Science of ETH Zurich is developing new software tools that are of potential use in various fields of science. You can find links to executable programs, source code, and documentation that you are encouraged to use. All software is free of charge.

LOCI (Laboratory for Optical and Computational Instrumentation) at Winsconsin University, Madison, WI – USA are releasing a number of other useful packages, including:

• WiscScan: tool A DSP-based acquisition system for laser scanning microscopes.
• VisBio: tool designed for easy visualization and analysis of multidimensional image data.
• Slim Plotter: a tool for visualization and analysis of spectral lifetime data.
• Data Converter: a utility for converting multidimensional image series between formats.

And also many components and plugins (i.e. 4-D Data Browser for ImageJ). Software and tools developed according to OME (Open Microscopy Environment).

OME is a multi-site collaborative effort among academic labs and a number of commercial entities that produces open tools to support data management for biological light microscopy. Designed to interact with existing commercial software, all OME formats and software is free! Now available:

• OME Server: a Perl-based for visualising, managing, and analysing microscope images and metadata. It includes a web browser interface, a threshold segmentation and tracking application (called “findSpots”), a MatLab interface, support for VisBio, LDAP, BioFormats and much more.
• OMERO: a Java-based server/client system for visualising, managing, and annotating microscope images and metadata.
• Bio-Formats– a Java library for reading and writing popular microscopy file formats capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats (maintained in collaboration with LOCI, http://loci.wisc.edu/).
• OME-TIFF: a specification and libraries for standardised image files for biological microscopy.

All of these are active development projects that respond to users’ requests and needs. The different websites provide facilities for download and feedback. Developers please to use and abuse!

Easy and light free microscopy and flow cytometry softwares for deconvolution (for remote batch restorations, using Huygens2 from ?SVI) and 3-D visualization, cell counting and mangament of flow cytometry data.

Imaging software from UCSB, University of California, Santa Barbara, CA – USA, from the Vision Research lab including:

• Bisque DataBase
• BioImage Convert
• Image Viewers
• bioView
• ITCN Image-based Tool for Counting Nuclei