BioImageXD - free open source 3D microscopy analysis and visualisation software - beta release
If you use VTK or other software for rendering 3D data, especially 3D
microscopy or medical data...
You can now download and use the windows beta version of BioImageXD!
BioImageXD is tailored for 3D microscopy, and is also useful for 2D
medical and other 3D data.
BioImageXD can read in numbered stacks of images, 8 bit grey scale
tiff images work best,
so generate a 3D data set (in fact a .vti file and a bxd header file.)
It will read carl zeiss .lsm files, some Leica files, and also import
stacks of 8 bit tiff and other image formats.
BioImageXD does interactive 3D volume rendering, and many other
viewing methods, and can also make movies/animations.
BioImageXD does colocalisation analysis, using the same algorithms as
in the WCIF ImageJ version.
BioImageXD is open source and free. We need your help to fix bugs and
add new features that YOU want!
Any offers of help with programming, processing/analysis algorithms,
funding etc very welcome.
BioImageXD is a collaborative open source free software project,
designed and developed by microscopists, cell biologists,
nanoscientists and programmers from the Universities of Jyväskylä and
Turku in Finland, and collaborators worldwide.
BioImageXD enables analysis, processing and 3D visualisation of multi
dimensional microscopy images on cheap and high end computer
hardware. Current commercially available software for microscopy
often has technical limitations, lack of features and flexibility,
annoying bugs, and prohibitively high cost. When users ask for new
features to be added or bugs to be fixed, this often takes years, or
never even happens. BioImageXD aims to match, and in some areas
outperform, commercial microscopy software in speed and
functionality, and do it for free. Further, since users drive the
development of the software, they can help add the features they
want, and fix bugs quickly.
Features in the beta version of BioImageXD released today include
image processing and statistical analysis, 3D visualisation and a
video editor module, the Animator, for producing fly through
animations of 3D microscopy data, allowing researchers to give the
best statistical and visual representation possible of their
microscopy results during scientific and media presentations.
Scientists on tight budgets will be able to take microscope images
and create informative pictures and impressive 3D movies. They can
save 10s of thousands of euros on software costs, and spend that on
microscope hardware instead, allowing them to produce high quality
science previously only attainable by very large centrally funded
government and industrial labs with microscopy core facilities.
BioImageXD is free and open source, much like the Linux computer
operating system project, and anyone can contribute to develpoment.
We aim to build an active community of users and developers of
BioImageXD, who will advocate use of BioImageXD as a replacement for
inflexible expensive commercial software, and drive the development
of BioImageXD to include the features they want and need, quickly. We
plan to build on the success of free software projects in science,
such as Linux, PyMol, ImageJ, VTK and Osirix, to name but a few.
The project website at http://www.bioimagexd.org hosts BioImageXD
downloadable as a Microsoft WindowsXP installer program and also as
source code. Soon to follow are Linux and Apple Mac OS X versions of
BioImageXD, and we are developing support for modern 64-bit
processors, high performance super computers and computing clusters/
BioImageXD is a new wave in the modern era of informational biology.
Researchers will be able to use free software for complex tasks
previously requiring expensive software purchases. Researchers will
get the tools they want and need in return for participation in the
BioImageXD development community.
Dr. Daniel James White BSc. (Hons.) PhD
Nanoscience Centre and Department of Biological and Environmental
Division of Molecular Recognition
PO Box 35
University of Jyväskylä