SpatTrack: an imaging toolbox for analysis of vesicle motility and distribution in living cells.

Frederik Wendelboe Lund, Marie Louise Jensen, Tanja Christensen, Gitte Krogh Nielsen, Christian Würtz Heegaard, Daniel Wüstner

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

The endocytic pathway is a complex network of highly dynamic organelles, which has been traditionally studied by quantitative fluorescence microscopy. The data generated by this method can be overwhelming and its analysis, even for the skilled microscopist, is tedious and error-prone. We developed SpatTrack, an open source, platform-independent program collecting a variety of methods for analysis of vesicle dynamics and distribution in living cells. SpatTrack performs 2D particle tracking, trajectory analysis and fitting of diffusion models to the calculated mean square displacement. It allows for spatial analysis of detected vesicle patterns including calculation of the radial distribution function and particle-based colocalization. Importantly, all analysis tools are supported by Monte Carlo simulations of synthetic images. This allows the user to assess the reliability of the analysis and to study alternative scenarios. We demonstrate the functionality of SpatTrack by performing a detailed imaging study of internalized fluorescence-tagged Niemann Pick C2 (NPC2) protein in human disease fibroblasts. Using SpatTrack, we show that NPC2 rescued the cholesterol-storage phenotype from a subpopulation of late endosomes/lysosomes (LE/LYSs). This was paralleled by repositioning and active transport of NPC2-containing vesicles to the cell surface. The potential of SpatTrack for other applications in intracellular transport studies will be discussed.
Original languageEnglish
Article numbertra.12228
JournalTraffic
Volume15
Issue number12
Pages (from-to)1406-29
Number of pages25
ISSN1398-9219
DOIs
Publication statusPublished - 16. Oct 2014

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Cells
Imaging techniques
Spatial Analysis
Fluorescence microscopy
Complex networks
Fibroblasts
Fluorescence Microscopy
Distribution functions
Fluorescence
Cholesterol
Trajectories
Proteins
Monte Carlo simulation
human NPC2 protein

Keywords

  • Bayesian; cholesterol efflux; convex hull; lysosome; Monte Carlo; Niemann Pick disease; particle tracking; pattern analysis; radial distribution function; spatial statistics

Cite this

Lund, Frederik Wendelboe ; Jensen, Marie Louise ; Christensen, Tanja ; Nielsen, Gitte Krogh ; Heegaard, Christian Würtz ; Wüstner, Daniel. / SpatTrack: an imaging toolbox for analysis of vesicle motility and distribution in living cells. In: Traffic. 2014 ; Vol. 15, No. 12. pp. 1406-29.
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abstract = "The endocytic pathway is a complex network of highly dynamic organelles, which has been traditionally studied by quantitative fluorescence microscopy. The data generated by this method can be overwhelming and its analysis, even for the skilled microscopist, is tedious and error-prone. We developed SpatTrack, an open source, platform-independent program collecting a variety of methods for analysis of vesicle dynamics and distribution in living cells. SpatTrack performs 2D particle tracking, trajectory analysis and fitting of diffusion models to the calculated mean square displacement. It allows for spatial analysis of detected vesicle patterns including calculation of the radial distribution function and particle-based colocalization. Importantly, all analysis tools are supported by Monte Carlo simulations of synthetic images. This allows the user to assess the reliability of the analysis and to study alternative scenarios. We demonstrate the functionality of SpatTrack by performing a detailed imaging study of internalized fluorescence-tagged Niemann Pick C2 (NPC2) protein in human disease fibroblasts. Using SpatTrack, we show that NPC2 rescued the cholesterol-storage phenotype from a subpopulation of late endosomes/lysosomes (LE/LYSs). This was paralleled by repositioning and active transport of NPC2-containing vesicles to the cell surface. The potential of SpatTrack for other applications in intracellular transport studies will be discussed.",
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SpatTrack: an imaging toolbox for analysis of vesicle motility and distribution in living cells. / Lund, Frederik Wendelboe; Jensen, Marie Louise ; Christensen, Tanja; Nielsen, Gitte Krogh; Heegaard, Christian Würtz; Wüstner, Daniel.

In: Traffic, Vol. 15, No. 12, tra.12228, 16.10.2014, p. 1406-29.

Research output: Contribution to journalJournal articleResearchpeer-review

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T1 - SpatTrack: an imaging toolbox for analysis of vesicle motility and distribution in living cells.

AU - Lund, Frederik Wendelboe

AU - Jensen, Marie Louise

AU - Christensen, Tanja

AU - Nielsen, Gitte Krogh

AU - Heegaard, Christian Würtz

AU - Wüstner, Daniel

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AB - The endocytic pathway is a complex network of highly dynamic organelles, which has been traditionally studied by quantitative fluorescence microscopy. The data generated by this method can be overwhelming and its analysis, even for the skilled microscopist, is tedious and error-prone. We developed SpatTrack, an open source, platform-independent program collecting a variety of methods for analysis of vesicle dynamics and distribution in living cells. SpatTrack performs 2D particle tracking, trajectory analysis and fitting of diffusion models to the calculated mean square displacement. It allows for spatial analysis of detected vesicle patterns including calculation of the radial distribution function and particle-based colocalization. Importantly, all analysis tools are supported by Monte Carlo simulations of synthetic images. This allows the user to assess the reliability of the analysis and to study alternative scenarios. We demonstrate the functionality of SpatTrack by performing a detailed imaging study of internalized fluorescence-tagged Niemann Pick C2 (NPC2) protein in human disease fibroblasts. Using SpatTrack, we show that NPC2 rescued the cholesterol-storage phenotype from a subpopulation of late endosomes/lysosomes (LE/LYSs). This was paralleled by repositioning and active transport of NPC2-containing vesicles to the cell surface. The potential of SpatTrack for other applications in intracellular transport studies will be discussed.

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