A new Python library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton

J Nunez-Iglesias; AJ Blanch; O Looker; MW Dixon; L Tilley

Journal article

A new Python library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton

J Nunez-Iglesias, AJ Blanch, O Looker, MW Dixon, L Tilley

Peerj | PEERJ INC | Published : 2018

DOI: 10.7717/peerj.4312

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Abstract

We present Skan (Skeleton analysis), a Python library for the analysis of the skeleton structures of objects. It was inspired by the "analyse skeletons" plugin for the Fiji image analysis software, but its extensive Application Programming Interface (API) allows users to examine and manipulate any intermediate data structures produced during the analysis. Further, its use of common Python data structures such as SciPy sparse matrices and pandas data frames opens the results to analysis within the extensive ecosystem of scientific libraries available in Python. We demonstrate the validity of Skan's measurements by comparing its output to the established Analyze Skeletons Fiji plugin, and, wit..

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University of Melbourne Researchers

Matthew Dixon Author

Leann Tilley Author

Related Projects (3)

BIO-METROLOGY AND MODELLING OF A COMPLEX SYSTEM: THE MALARIA PARASITE

Bio-metrology and modelling of a complex system: the malaria parasite: This fellowship project aims to develop a cross-disciplinary program ..

BIO-METROLOGY AND MODELLING OF A COMPLEX SYSTEM: THE MALARIA PARASITE (UM CASH CONTRIBUTIONS)

This fellowship project aims to develop a cross-disciplinary program to measure, model and manipulate a complex cellular system — sexual dif..

BIO-METROLOGY AND MODELLING OF A COMPLEX SYSTEM: THE MALARIA PARASITE (GEORGINA SWEET FUND)

This fellowship project aims to develop a cross-disciplinary program to measure, model and manipulate a complex cellular system — sexual dif..

Grants

Awarded by Australian Research Council

Funding Acknowledgements

This work was supported by the Australian Research Council (grant number FL150100106). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.