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Acquiarium Download PDF Print

Terms of use

Acquiarium is open source software licensed under the GNU General Public License (GPL).

Downloads are protected by login and password which you may obtain after filling the Registration form.  We require the registration to be able to demonstrate the demand for software to grant agencies and therefore keep the project growing.

If you publish results where the software was employed, you can cite the following article.

[1] P. Matula, M. Maška, O. Daněk, P. Matula, M. Kozubek, "Acquiarium: Free Software for Acquisition and Analysis of 3D Images of Cells in Fluorescence Microscopy", 6th IEEE International Symposium on Biomedical Imaging, Boston, 2009.


Acquiarium can be downloaded of different versions and configurations. Click on Acquiarium versions to see the overview of Acquiarium changes. The configurations of the software are described in the relevant sections bellow.

To install the software on Windows XP run the installer on your machine and follow the installation wizard.

Windows XP (no hardware configuration)

These versions are configured for image analysis on workstations. The versions do not contain any hardware driver. One can open depositories acquired using Acquiarium, import images using import plugin, browse, view and explore images, carry out image corrections, batch-crop images, analyze images, visualize results and export measurements into text files.

The versions 'with Bioformats support' contains LOCI Bio-Formats library. The library can be used for importing a large number of microscopy formats. You will need Java Runtime Environment (JRE) before installing these versions. If it is not installed on your machine the wizard will guide you how to do it.

The versions 'without Bioformats support' use our i3d library only for reading the images (it supports ICS - Image Cytometry Standard, TIFF, TARGA, JPEG, and METAIO image formats). You don't need to have Java Runtime Environment (JRE) installed.


Latest version built on June 12, 2012 - with Bioformats support
Latest version built on June 12, 2012 - without Bioformats support

Former version built on August 26, 2011 - with Bioformats support
Former version built on August 26, 2011 - without Bioformats support

Windows XP (configurations with hardware support)

If you are interested in a version with hardware support, please contact us at cbia-info(at)


Download the source codes and build it yourself.

Source codes

Please write e-mail to cbia-info(type 'at' sigh here) and we will send you the source codes.


Testing data

Sample depository containing four volumes of interest.

We recommend visiting the tutorial page for Acquiarium quick start.

Written by Pavel Matula   
Last Updated ( Wednesday, 13 June 2012 )
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