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CytoSpectre: a tool for spectral analysis of oriented structures on cellular and subcellular levels

Overview of attention for article published in BMC Bioinformatics, October 2015
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Title
CytoSpectre: a tool for spectral analysis of oriented structures on cellular and subcellular levels
Published in
BMC Bioinformatics, October 2015
DOI 10.1186/s12859-015-0782-y
Pubmed ID
Authors

Kimmo Kartasalo, Risto-Pekka Pölönen, Marisa Ojala, Jyrki Rasku, Jukka Lekkala, Katriina Aalto-Setälä, Pasi Kallio

Abstract

Orientation and the degree of isotropy are important in many biological systems such as the sarcomeres of cardiomyocytes and other fibrillar structures of the cytoskeleton. Image based analysis of such structures is often limited to qualitative evaluation by human experts, hampering the throughput, repeatability and reliability of the analyses. Software tools are not readily available for this purpose and the existing methods typically rely at least partly on manual operation. We developed CytoSpectre, an automated tool based on spectral analysis, allowing the quantification of orientation and also size distributions of structures in microscopy images. CytoSpectre utilizes the Fourier transform to estimate the power spectrum of an image and based on the spectrum, computes parameter values describing, among others, the mean orientation, isotropy and size of target structures. The analysis can be further tuned to focus on targets of particular size at cellular or subcellular scales. The software can be operated via a graphical user interface without any programming expertise. We analyzed the performance of CytoSpectre by extensive simulations using artificial images, by benchmarking against FibrilTool and by comparisons with manual measurements performed for real images by a panel of human experts. The software was found to be tolerant against noise and blurring and superior to FibrilTool when analyzing realistic targets with degraded image quality. The analysis of real images indicated general good agreement between computational and manual results while also revealing notable expert-to-expert variation. Moreover, the experiment showed that CytoSpectre can handle images obtained of different cell types using different microscopy techniques. Finally, we studied the effect of mechanical stretching on cardiomyocytes to demonstrate the software in an actual experiment and observed changes in cellular orientation in response to stretching. CytoSpectre, a versatile, easy-to-use software tool for spectral analysis of microscopy images was developed. The tool is compatible with most 2D images and can be used to analyze targets at different scales. We expect the tool to be useful in diverse applications dealing with structures whose orientation and size distributions are of interest. While designed for the biological field, the software could also be useful in non-biological applications.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 67 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 67 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 18 27%
Researcher 13 19%
Student > Master 6 9%
Student > Doctoral Student 5 7%
Student > Bachelor 3 4%
Other 4 6%
Unknown 18 27%
Readers by discipline Count As %
Agricultural and Biological Sciences 11 16%
Engineering 11 16%
Biochemistry, Genetics and Molecular Biology 10 15%
Medicine and Dentistry 4 6%
Computer Science 2 3%
Other 10 15%
Unknown 19 28%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 04 November 2015.
All research outputs
#15,349,419
of 22,831,537 outputs
Outputs from BMC Bioinformatics
#5,377
of 7,288 outputs
Outputs of similar age
#166,664
of 284,375 outputs
Outputs of similar age from BMC Bioinformatics
#111
of 156 outputs
Altmetric has tracked 22,831,537 research outputs across all sources so far. This one is in the 22nd percentile – i.e., 22% of other outputs scored the same or lower than it.
So far Altmetric has tracked 7,288 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.4. This one is in the 18th percentile – i.e., 18% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 284,375 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 32nd percentile – i.e., 32% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 156 others from the same source and published within six weeks on either side of this one. This one is in the 21st percentile – i.e., 21% of its contemporaries scored the same or lower than it.