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