This article is a little bit outdated. Up-to-date pieces of information are available on Acquiarium homepage.

Acquiarium is an image acquisition and analysis software for high-resolution 3D cytometry. Its main goal is to provide a tool for high-quality evaluation of spatial arrangement of targets in large number of fluorescently labeled cells. The idea is to link high-throughput acquisition using spinning-disk system with appropriate software tools for automated 3D image analysis. Acquiarium is the successor of FISH software package.

The first version of Acquiarium software has been finished and released in the fall of 2007.
Although preliminary versions of the software have been tested and employed in CBIA and LMCC laboratories throughout the whole development process, Acquiarium version 1.0 is the first self-contained version that can solve tasks in 3D image cytometry (e.g. FISH dots analysis and spatial analysis of chromosome territories). This article describes the main features of Acquiarium version 1.0.

The software download is free of charge.

Main Features

Acquiarium provides means for high-throughput image acquisition, image correction and automated image analysis. All data concerning one experiment are stored in a depository. The depository contains raw images, description of channels (visualized targets) on a slide, corrected images, user and hardware parameters used throughout the experiment, logs etc.

List of features:

• The software can run in different hardware profiles.
• Dummy drivers for simulation of acquisition.
• Database of fluorochromes and suitable filters installed on the system.
• Logging of important parameters.
• Number of channels in depository is not limited by software.
• Wide camera control.
• Camera binning can differ throughout channels.
• Acquisition parameters can be locked through all channels.
• Detection and visualization of underexposed and overexposed pixels.
• Support for 8-bit as well as 16-bit images (stored in ICS format).
• Full coordinates (x,y,z) are stored for slides and can be relocated (repeated acquisition).
• Acquisition of CCD regions supported.
• Auto-focusing routine.
• On-line histogram.
• Support for uneven illumination correction.
• Deconvolution and chromatic aberration correction is solved by external packages.
• Several scanning modes.
• Maximal intensity and 3D viewer of raw as well as corrected images.
• User can define Region Of Interests (ROIs).
• Batch-cropping of ROIs.
• Several image analysis algorithms (thresholding based methods, k-mean clustering methods, Chan-Vese segmentation, EMAX segmentation).
• Segmentation results are stored in groups for easy manipulation.
• Overlay of segmentation results on image data.
• Computation of local histogram.
• Export of segmentation results in text files (volume, surface, roundness factor, weighted center, local radius, mutual distances between objects, object overlapping ratio).
• Import/export to FISH 2.0.
  

• Import from Batchcrop.

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