Free open source software for analysis and visualization of multidimensional biomedical images


Is there a manual / more user instructions available?
There is a concise Getting Started guide available, describing all central features with pictures, tips and step-by-step instructions. The guide is accessible from here or in BioImageXD from the question mark button in the main toolbar or from the Help menu. The software itself contains on-screen descriptions for most features (appearing on shaded background), including possible inputs and outputs for procedures that can be pipelined. In addition, following Webinar teaches how to use BioImageXD in practice:

How do I cite BioImageXD?
The 2012 Nature Methods paper is the principal publication for BioImageXD, please cite it whenever referring to the software:

P. Kankaanpää, L. Paavolainen, S. Tiitta, M. Karjalainen, J. Päivärinne, J. Nieminen, V. Marjomäki, J. Heino and D. J. White (2012). BioImageXD: an open, general-purpose and high-throughput image-processing platform. Nature Methods 9 (7): 683-689. DOI: 10.1038/nmeth.2047.

Please let us know by emailing This email address is being protected from spambots. You need JavaScript enabled to view it. when you cite BioImageXD, as this helps us develop and maintain the software.

Why are some features and settings colored red in the GUI?
Things in red are for expert users only. Novice users are recommended not to use features/settings colored in red. Instead of hiding expert settings or making different versions for different users, we feel that it is better to show all available details to all users, and to use the color coding to guide beginners.

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 as well as MRC file format used for electron microscopy. BioImageXD also supports the open standard OME-TIFF file format. Other file types can be imported as regular images (TIFF, PNG and so on).

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 slice, gallery, orthographical sections and projection 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 reduction and other types of processing, and you can even do automated tracking of segmented objects. Batch processing enables easy processing of large data amounts. None of the features of BioImageXD require programming skills.

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. For large datasets, we recommend 64-bit versions of the software. Currently supported operating systems are Windows XP, Vista and 7, Mac OS X 10.6/10.7 and Linux. We provide 64-bit packages for all the supported operating systems, and also a 32-bit package for Windows.

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 email address is being protected from spambots. You need JavaScript enabled to view it..

BioImageXD wants to send an automatically generated bug report, and is asking me what to do?
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 therefore encourage everyone to allow the sending of the reports, because they are of great help to us in fixing bugs with the software. Those who want to get a personal reply about the bug report can include their email address.

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. 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 - in this case we would be very happy if you could share your fix with others.

Can I trust the results I get with BioImageXD?
BioImageXD is not certified for diagnostic use or other purposes in which the lives or well-being of people might be at stake directly. 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 erroneous results, but this is the case with any software. If you notice anything suspicious, please let us know, and we will look into it. Importantly, BioImageXD contains simulation tools that can create simulated image data, which can be used to verify results.

How can I contribute to the making of BioImageXD?
Basically, in any way you like! You can for instance do testing and bug reporting, program a new feature or improve and modify existing features. We are grateful to anyone who shares their new features or fixes. If you wish to do more development for the platform, contact us at This email address is being protected from spambots. You need JavaScript enabled to view it. so we will provide you developer access to the repository.

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