News

May 19, 2016: Version 1.2 of CytoSpectre released. The update fixes occasional issues in cell-by-cell analysis. See the corresponding technical note for details.

April 21, 2016: Version 1.1 of CytoSpectre released. The update fixes minor bugs in the command line interface and GUI. Analysis results remain unaffected by the update.

February 15, 2016: Risto-Pekka will present CytoSpectre at the Cardiac Development, Regeneration and Repair meeting, April 3-7, 2016 in Snowbird, Utah, USA.

January 15, 2016: Risto-Pekka will present CytoSpectre at the 8th Kauppi Science Day on February 11th in Tampere, Finland.

December 4, 2015: Risto-Pekka presented CytoSpectre at the BioMediTech Research Day 2015 in Tampere, Finland.

October 26, 2015: The CytoSpectre paper was published in BMC Bioinformatics.

October 15, 2015: The CytoSpectre paper was accepted in BMC Bioinformatics.

About

CytoSpectre is a software tool for the analysis of orientation and wavelength distributions from micrographs. It is based on spectral analysis and allows analyzing various structures of different dimensions e.g. clusters of cells or intracellular fibrillar assemblies. In principle, CytoSpectre is compatible with 2D images obtained using any form of microscopy. In addition to quantifying the mean orientation of the structures of interest, estimates of parameters describing the anisotropy and shape of the distributions can also be obtained. A similar analysis can be performed for wavelength distributions, which describe the dimensions of the target structures.

CytoSpectre is implemented in MATLAB, but a deployed application for Windows is also freely available for academic use. The software can be operated on basic hardware via a graphical user interface or the MATLAB command line. Analysis results can be easily exported to spreadsheets or text files for further study or plotted as images for visualization purposes.

If you use CytoSpectre in a publication, please cite the following article:
Kimmo Kartasalo, Risto-Pekka Pölönen, Marisa Ojala, Jyrki Rasku, Jukka Lekkala, Katriina Aalto-Setälä, Pasi Kallio. CytoSpectre: a tool for spectral analysis of oriented structures on cellular and subcellular levels, BMC Bioinformatics 2015, 16:344.

Download

Users with a MATLAB installation can download the CytoSpectre source code. Note that CytoSpectre requires the following toolboxes: Signal Processing Toolbox, Image Processing Toolbox, Statistics and Machine Learning Toolbox, and Curve Fitting Toolbox. CytoSpectre was developed and tested with MATLAB R2014a but is known to be compatible with newer versions as well.

Users without a MATLAB installation should download the deployed application. The deployed application can be operated without a MATLAB installation by installing the free MATLAB Compiler Runtime (MCR) 8.3 libraries, which can normally be downloaded automatically during the installation process. If you have trouble obtaining the MCR, you can also download the larger package which contains both the deployed application itself and the MCR. The deployed application was developed and tested for Windows 7 but has been reported to be compatible with newer Windows releases as well.

Version 1.2 (Updated cell-by-cell analysis)
MATLAB (R2014a) source code
Windows 7 (64-bit) deployed application
Windows 7 (64-bit) deployed application and MCR 8.3
Technical Note 1

Version 1.1 (Minor bugfixes to the user interface)
MATLAB (R2014a) source code
Windows 7 (64-bit) deployed application
Windows 7 (64-bit) deployed application and MCR 8.3

Version 1.0 (Initial release)
MATLAB (R2014a) source code
Installation packages for version 1.0 are provided upon request.

Instructions on using CytoSpectre are given in the user guide.

CytoSpectre in MATLAB source code form is licensed under the GNU General Public License (GPL). The CytoSpectre deployed application is governed by the MathWorks MCR license and applicable parts of The MathWorks, Inc. Software License Agreement. Using the CytoSpectre deployed application for commercial purposes is prohibited. CytoSpectre also utilizes the CircStat toolbox by Philipp Berens, which is governed by the corresponding license.

Example images are provided for trying out the software:
- Test set 1: 15 widefield fluorescence microscopy images of iPS-derived cardiomyocytes stained for troponin T (red), alpha actinin (green) and with DAPI (blue).
- Test set 2: 15 widefield fluorescence microscopy images of iPS-derived carciomyocytes stained for troponin T (red), myosin binding protein C3 (green) and with DAPI (blue).
- Test set 3: 15 phase contrast microscopy images of iPS-derived peripheral sensory neurons.

Publications

Kartasalo, Kimmo, et al. "CytoSpectre: a tool for spectral analysis of oriented structures on cellular and subcellular levels." BMC Bioinformatics 16.1 (2015): 344.

Contact

Don't hesitate to contact us if you spot any bugs or need help for using CytoSpectre in your application!

Kimmo Kartasalo
kimmo.kartasalo (at) tuni.fi

Risto-Pekka Pölönen
risto-pekka.polonen (at) tuni.fi

Pasi Kallio
pasi.kallio (at) tuni.fi

Links

BioMediTech - Institute of Biosciences and Medical Technology

Tampere University