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

PeerJ
Juan Nunez-IglesiasLeann Tilley

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.

References

Oct 12, 2000·IEEE Transactions on Medical Imaging·P J YimR M Summers
Mar 17, 2010·Microscopy Research and Technique·Ignacio Arganda-CarrerasCarlos Ortiz-De-Solorzano
Sep 10, 2011·Molecular & Cellular Proteomics : MCP·Melanie G MillhollandDoron C Greenbaum
Nov 22, 2011·Biophysical Journal·Andrea NansDavid L Stokes
Jul 16, 2014·PeerJ·Stéfan van der WaltUNKNOWN scikit-image contributors
Apr 29, 2015·Proceedings of the National Academy of Sciences of the United States of America·Yao ZhangSubra Suresh
Apr 14, 2016·Proceedings of the National Academy of Sciences of the United States of America·Megan DearnleyLeann Tilley

❮ Previous
Next ❯

Citations

Sep 6, 2019·Microbiology and Molecular Biology Reviews : MMBR·Jan D Warncke, Hans-Peter Beck
May 17, 2019·Current Osteoporosis Reports·Richard WeinkamerPeter Fratzl
Feb 28, 2021·Annals of the New York Academy of Sciences·Martin PfisterRené M Werkmeister
May 6, 2021·Journal of Biophotonics·Vladimir A BaulinXavier Le Guével

❮ Previous
Next ❯

Methods Mentioned

BETA
quartz crystal microbalance
scanning electron microscopy
atomic
transmission electron microscopy

Software Mentioned

Analyze
correlate
SciPy
Excel
Skan
pyplot
sparse
Analyze Skeletons
Fiji Analyze Skeletons
Python Package Index (

Related Concepts

Related Feeds

Antimalarial Agents (ASM)

Antimalarial agents, also known as antimalarials, are designed to prevent or cure malaria. Discover the latest research on antimalarial agents here.

Antimalarial Agents

Antimalarial agents, also known as antimalarials, are designed to prevent or cure malaria. Discover the latest research on antimalarial agents here.