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

MUCIC - Masaryk University Cell Image Collection

Colon Tissue (fixed cells)

Here, you can find 30 synthetic images of human colon tissue including ground truth (foreground/background)  images. The dataset was generated using the virtual microscope imitating the microscope Zeiss S100 (objective Zeiss 63x/1.40 Oil DIC) attached to confocal unit Atto CARV and CCD camera Micromax 1300-YHS. The image data was saved using three different file formats: ICS, HDF5 and 3D-TIFF. Please, feel free to select the format you prefer. All of them contain the same data. The individual image files are aggregated in ZIP archives.

Example images:

3D image 3D foreground


If you use this dataset in your research papers, please refer the following article:

  • Svoboda D., Homola O., Stejskal S. Generation of 3D Digital Phantoms of Colon Tissue, In International Conference on Image Analysis and Recognition - ICIAR 2011, Part II, LNCS 6754, Berlin, Heidelberg: Springer-Verlag, pp 31-39, June 2011, ISBN 978-3-642-21595-7 

This research was supported by the Ministry of Education of the Czech Republic (Projects No. LC535 and No. 2B06052).
 


HL60 Cell Line (fixed cells)

Here, you can find 30 synthetic images of nuclei of HL60 cell line including ground truth (foreground/background) images. Each image set contains 20 cell nuclei with specified probability of clustering (0%, 25%, 50%, and 75%). The dataset was generated using the virtual microscope imitating the microscope Zeiss S100 (objective Zeiss 63x/1.40 Oil DIC) attached to confocal unit Atto CARV and CCD camera Micromax 1300-YHS. The image data was saved using three different file formats: ICS, HDF5 and 3D-TIFF. Please, feel free to select the format you prefer. All of them contain the same data. The individual image files are aggregated in ZIP archives.

Example images:

3D image 3D foreground


If you use this dataset in your research papers, please refer the following article:

  • Svoboda D., Kozubek M., Stejskal S. Generation of Digital Phantoms of Cell Nuclei and Simulation of Image Formation in 3D Image Cytometry, Cytometry Part A, Volume 75A, Issue 6, pp 494-509, June 2009, ISSN:1552-4922 

This research was supported by the Ministry of Education of the Czech Republic (Projects No. LC535 and No. 2B06052).



Granulocytes (fixed cells)

Here, you can find 30 synthetic images of nuclei of granulocytes including ground truth (foreground/background) images. Each image set contains up to 15 cell nuclei. The dataset was generated using the virtual microscope imitating the microscope Zeiss S100 (objective Zeiss 63x/1.40 Oil DIC) attached to confocal unit Atto CARV and CCD camera Micromax 1300-YHS. The image data was saved using three different file formats: ICS, HDF5 and 3D-TIFF. Please, feel free to select the format you prefer. All of them contain the same data. The individual image files are aggregated in ZIP archives.

Example images:

3D image 3D foreground

 

If you use this dataset in your research papers, please refer the following article:

  • Svoboda D., Kozubek M., Stejskal S. Generation of Digital Phantoms of Cell Nuclei and Simulation of Image Formation in 3D Image Cytometry, Cytometry Part A, Volume 75A, Issue 6, pp 494-509, June 2009, ISSN:1552-4922

This research was supported by the Ministry of Education of the Czech Republic (Projects No. LC535 and No. 2B06052).


Time-lapse Image Sequences (living cells)

In this section, you can find a reference to collection of computer generated time-lapse image sequences of nuclei of HL60 cells stained with Hoescht (both 2D & 3D). The dataset was generated with the help of our virtual microscope. The dataset was prepared for the 1st a the 2nd edition of Cell Tracking Challenge joined to IEEE International Symposium on Biomedical Imaging.

Example image sequence:


The data is available for free at this address:

http://www.codesolorzano.com/Challenges/CTC/Datasets.html

If you use this dataset in your research papers, please refer one of the following articles: 

  • Svoboda, D. Ulman V. MitoGen: A Framework for Generating 3D Synthetic Time-Lapse Sequences of Cell Populations in Fluorescence Microscopy. IEEE Transactions on Medical Imaging, IEEE Engineering in Medicine and Biology Society, Volume 36, Issue 1, Jan 2017, available on-line: http://dx.doi.org/10.1109/TMI.2016.2606545
  • Maška M, Ulman V, Svoboda D, Matula P, Matula P, Ederra C, Urbiola A, España T, Venkatesan S, Balak DM, Karas P, Bolcková T, Štreitova M, Carthel C, Coraluppi S, Harder N, Rohr K, Magnusson KE, Jaldén J, Blau HM, Dzyubachyk O, Křížek P, Hagen GM, Pastor-Escuredo D, Jimenez-Carretero D, Ledesma-Carbayo MJ, Muñoz-Barrutia A, Meijering E, Kozubek M, Ortiz-de-Solorzano C. A benchmark for comparison of cell tracking algorithms, Bioinformatics, Volume 30(11), pp 1609-1617, June 2014

This research was supported by the Czech Science Foundation, Grant No. GA14-22461S.


Vaculogenesis (living cells)

Here, you can find the sequence of frames recording the process called vasculogenesis. The endothelial cells, initially spread across the glass slide, tend to attach each other and form the networks with thin and elongated chords. This process forces some cells to be markedly elongated, as can be seen in the figure below. The dataset was generated with the help of our virtual microscope.

Example images:

3D image 3D foreground
 

If you use this dataset in your research papers, please refer the following article:  

  • Svoboda D, Ulman V, Kováč P, Šalingová B, Tesařová L, Koutná IK, Matula P. Vascular Network Formation in Silico Using the Extended Cellular Potts Model, In IEEE International Conference on Image Processing, Phoenix, Arizona (USA), 2016, pp. 3180-3183, ISBN 978-1-4673-9961-6.

This research was supported by the Czech Science Foundation, Grant No. GA14-22461S.



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