[vtkusers] BioImageXD - free open source 3D microscopy analysis and visualisation software - beta release

[Dan White]

Dear All,

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.

http://www.bioimagexd.org
follow the download link at the top of the page.

email to info at bioimagexd.org


Enjoy the software!

BioImageXD team


Release of BioImageXD - Press release

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/ 
grids.

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
Bioimaging Coordinator
Nanoscience Centre and Department of Biological and Environmental  
Sciences
Division of Molecular Recognition
Ambiotica C242
PO Box 35
University of Jyväskylä
Jyväskylä
FIN 40014
Finland

+358 14 260 4183 (work)
+358 468102840 (mobile)
http://www.bioimagexd.org
http://www.chalkie.org.uk
dan at chalkie.org.uk
white at cc.jyu.fi