B i o I m a g e X D

Is there a manual / more user instructions available somewhere?

Yes, there is a user manual. It is comprehensive but not yet fully completed. You can download it here.

How do I cite BioImageXD?

Peer reviewed publications on BioImageXD are currently under preparation and not yet available. In the mean time please cite BioImageXD using our URL as follows: 

Kankaanpää, P., Pahajoki, K., Marjomäki, V., Heino, J., White, D. BioImageXD (2006) on World Wide Web http://www.bioimagexd.net 

If your journal does not accept URL citations, cite BioImageXD as a published computer program: 

Kankaanpää, P., Pahajoki, K., Marjomäki, V., Heino, J., White, D. BioImageXD (2006) University of Jyväskylä, Jyväskylä, Finland and University of Turku, Turku, Finland 

or simply: 

Kankaanpää, P., Pahajoki, K., Marjomäki, V., Heino, J., White, D. BioImageXD (2006)  

Another option is to cite a non peer reviewed review-type article on BioImageXD, preferrably the one in Microscopy Today: 

Kankaanpää, P., Pahajoki, K., Marjomäki, V., Heino, J., White, D. (2006) BioImageXD – New Open Source Free Software for the Processing, Analysis and Visualization of Multidimensional Microscopic Images. Microscopy Today, 14(3): 12-16. 

or like this: 

Please do let us know ( This e-mail address is being protected from spam bots, you need JavaScript enabled to view it ) if you cite BioImageXD, so that we can keep track of how the software is being used. Thanks!

What type of images or data is BioImageXD suitable for?

Basically any multidimensional image data (in the form of a "stack" of "slices") or a single image file can be loaded and processed. However, BioImageXD is optimized for confocal and fluorescence microscopy image data. Many common microscopy file formats are supported, meaning that you can open files produced by for instance Zeiss, Leica and Olympus confocals directly. Other file types can be imported as regular images (TIFF, JPEG and so on). In the future file format support and analysis tools will be expanded to better cover for instance electron microscope tomography and atomic force microscopy.

What exactly can I do with BioImageXD?

BioImageXD contains a huge amount of features, ranging from visualizing your data in numerous ways to analyzing and quantifying it with some of the most sophisticated algorithms available. Visualization tools include for instance slice, gallery and orthographical sections views as well as full, interactive 3D rendering tools with surface and volume rendering algorithms. You can also create fancy animations with the built in animator. Analysis tools include some of the most comprehensive colocalization and segmentation tools available. There is also a collection of dozens of filters for noise removal and other types of processing, and you can even do automated tracking of segmented objects. Script recording functions enable easy processing of large data amounts. See the user manual for more information on the various features.

What type of computers does BioImageXD run on?

Any regular office or home computer/laptop should do, but obviously the more memory and processor power you have, the better. Currently supported operating systems are Windows XP, Mac OS X and Linux.

I encountered a malfunction, error or problem. What do I do?

Please send us a bug report! The more details you can provide, the better and faster we will be able to fix the problem. You can find the bug tracking system here. You can also email us directly at This e-mail address is being protected from spam bots, you need JavaScript enabled to view it

BioImageXD wants to send an automatically generated bug report, and is asking me what to do?

Can I be sure you are not gathering personal information or anything like that if I allow the sending of the report? The report only contains the software configuration and actions leading to the problem. We guarantee that sending the report is completely safe, and no personal information of you or your computer is sent anywhere. We encourage everyone to allow the sending of the reports, because they are of great help to us in fixing problems with the software.

Why does BioImageXD contain errors and bugs?

All computer programs do, unfortunately. Sometimes bugs can be really annoying, but please bear in mind that BioImageXD is a huge open source project made with limited resources, and we cannot test everything as comprehensively as we'd like. Also, so far all releases of the software are beta versions, meaning that they are not finalized. (We\'d also like to point out, that many expensive commercial programs in this field often contain just as many bugs and errors...) We rely very much on our users to report bugs and errors to us, and would like to invite everyone to participate as well as they can. Together we can constantly improve BioImageXD! If you are able to, you can also freely try to fix any problems yourself - just remember to share your work, as expected by our license.

Can I trust the results I get with BioImageXD?

BioImageXD cannot be used for diagnostic or other purposes in which the lives or well being of people might be at stake. The usual disclaimer applies: BioImageXD is not certified or guaranteed to be fit for any particular purpose.  User Beware. For research purposes, however, the results are likely to be trustworthy and reliable. The biggest error source is unlikely to be a bug or malfunction in the software, but rather the user, choosing perhaps an incorrect tool or setting for the data being processed. Of course it is also always possible that there are erroneus results, but this is the case with any software. If you notice anything suspicious, please let us know, so we can try to fix it.

How can I contribute to the making of BioImageXD?

Basically, in any way you like! Just remember that you are expected to share your work as is stated in our license. You can for instance do testing and bug reporting, program a new feature or improve and modify existing features. It is advisable to contact us before doing anything major: This e-mail address is being protected from spam bots, you need JavaScript enabled to view it the reports, because they are of great help to us in fixing problems with the software.