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

Juan Nunez-Iglesias, Adam J. Blanch, Oliver Looker, Matthew W. Dixon, Leann Tilley

Research output: Contribution to journalArticleResearchpeer-review

7 Citations (Scopus)

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, with a new scanning electron microscopy (SEM)-based method, we confirm that the malaria parasite Plasmodium falciparum remodels the host red blood cell cytoskeleton, increasing the average distance between spectrin-actin junctions.

Original languageEnglish
Article numbere4312
Number of pages10
JournalPeerJ
Volume2018
Issue number2
DOIs
Publication statusPublished - 15 Feb 2018
Externally publishedYes

Keywords

  • Cytoskeleton
  • Malaria
  • Python
  • Red blood cell
  • Skeleton analysis

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