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CytoPacq PDF Print
Article Index
Simulated Phenomena
Execution and Downloading
MUCIC - Image Datasets
History of Changes


CytoPacq is a toolbox that consists of three individual modules: 3D-cytogen, 3D-optigen, and 3D-acquigen. Each one is a virtual machine capable of simulating selected real processes:

  • 3D-cytogen* ... a module generating the digital cell phantoms (spatial objects imitating cells and their components as well as their structure).
  • 3D-optigen ... a module simulating the transmission of the signal through the optical system.
  • 3D-acquigen ... a module simulating the phenomenons manifesting themselves during image capture with digital CCD cameras (various types of noise, sampling, digitization, etc.)

Composition of all these toolkits together into a single sequence forms a complex toolbox, which we call "CytoPacq". It covers the most common phenomenons appearing during each real acquisition process.

This module is responsible for digital phantom generation. Recently, four types of objects have been implemented: HL-60 cell nuclei, granulocyte nuclei, microspheres, and tissue colons. However, there is no restriction put on the number of objects and the object complexity. As soon as a suitable model is defined, the corresponding digital phantom can be simply generated. The current version of 3d-cytogen supports plugins, i.e. each user can implement his/her own digital phantom.

The second module (3d-optigen) simulates the optical system. Namely, it involves the blurring process occurring in the optical system. Aside from blur, the devitation of the illumination axis is also taken into account.

The last stage (3d-acquigen) imitates the job of the digital CCD camera. Here, the phenomenons like noise, sampling, and quantization are simulated.

(*) ... 3D-cytogen can be optionaly substituted with the alternative modules that are capable of generating the cell types with conceptually different structure from those generated in 3d-cytogen. These modules include:

  • TRAGen - Motility of population of living cells (2D+time)

    In order to imitate the behaviour of cells in densely populated microscopic slide, we developed a tool that allows for generating 2D image sequences showing simulated living cell populations together with ground-truth images for evaluation of cell tracking tasks. The simulated events include namely cell motion, cell division, cell death, and cell clustering up to tissue-level density. TRAgen features complete cell cycle with shape changes due to rounding and elongation of a cell just before its division. The user can add his own internal structure to simulate, for example, either fluorescently stained cells or cells as observed using phase-contrast microscopy.

  • MitoGen - Mitosis of living cells (3D+time)

    MitoGen is a complex module capable of generating the fully 3D time-lapse image sequences depicting the population of living cells. The typical events that can be observed include: cells division, cell motility, cell appearance and disappearance near the border of the region of interest. The data generated using the MitoGen is an integral part of training and testing dataset of the 1st a the 2nd edition of Cell Tracking Challenge joined to IEEE International Symposium on Biomedical Imaging.

  • Vasculogenesis - Formation of tubular networks (2D+time)

    This module allows to generate visually plausible synthetic image sequences of evolving fluorescently labeled vascular networks with ground truth data. Such generated datasets can be subsequently used for testing and validating methods employed for the analysis and measurement of the images of real vascular networks.

Written by David Svoboda   
Last Updated ( Wednesday, 23 August 2017 )
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