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

被引：50

作者：

Nunez-Iglesias, Juan ^{[1
]}

Blanch, Adam J. ^{[2
]}

Looker, Oliver ^{[2
]}

Dixon, Matthew W. ^{[2
]}

Tilley, Leann ^{[2
]}

机构：

[1] Univ Melbourne, Melbourne Bioinformat, Melbourne, Vic, Australia

[2] Univ Melbourne, Inst Bio21, Dept Biochem & Mol Biol, Melbourne, Vic, Australia

来源：

PEERJ | 2018年 / 6卷

基金：

澳大利亚研究理事会;

关键词：

!text type='Python']Python[!/text; Skeleton analysis; Malaria; Red blood cell; Cytoskeleton; RECONSTRUCTION;

D O I：

10.7717/peerj.4312

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：10

共 14 条

[11] Giant Host Red Blood Cell Membrane Mimicking Polymersomes Bind Parasite Proteins and Malaria Parasites
Najer, Adrian
Thamboo, Sagana
Palivan, Cornelia G.
Beck, Hans-Peter
Meier, Wolfgang
CHIMIA, 2016, 70 (04) : 288 - 291
[12] A novel strain energy relationship for red blood cell membrane skeleton based on spectrin stiffness and its application to micropipette deformation
Svetina, Sasa
Kokot, Gasper
Kebe, Tjasa Svelc
Zeks, Bostjan
Waugh, Richard E.
BIOMECHANICS AND MODELING IN MECHANOBIOLOGY, 2016, 15 (03) : 745 - 758
[13] A new ensemble learning approach to detect malaria from microscopic red blood cell images
Bhuiyan M.
Islam M.S.
Sensors International, 2023, 4
[14] The human malaria parasite Plasmodium falciparum exports the ATP-binding cassette protein PFGCN20 to membrane structures in the host red blood cell
Bozdech, Z
VanWye, J
Haldar, K
Schurr, E
MOLECULAR AND BIOCHEMICAL PARASITOLOGY, 1998, 97 (1-2) : 81 - 95

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