ViSP: representing single-particle localizations in three dimensions

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Figure 1: Visualization of 3D single-particle localizations with ViSP.

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Acknowledgements

We thank B. Hajj (Institut Curie), J. Chen (Janelia Farm Research Campus), I. Izeddin (Ecole Normale Supérieure), J. Sillibourne (Commissariat à l'Energie Atomique et aux Energies Alternatives) and M. Bornens (Institut Curie) for providing super-resolution data sets used in the figures of this correspondence. We are grateful to K. Busch (Universität Osnabrück) for sharing the plasmid TOM-20-GFP. We also thank N. Clack, F. Mueller and X. Darzacq for discussions during the preparation of this work. This work was supported by funding from the Transcription Imaging Consortium at the Janelia Farm Research Campus, the Institut Curie International PhD Program and by the Tridimic grant from the program Recherches Partenariales et Innovation Biomédicale from Agence Nationale pour la Recherche.

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Correspondence to Mohamed El Beheiry or Maxime Dahan.

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Supplementary information

Supplementary Software

ViSP executables for Windows and Mac OS X (with User Manual and License) (ZIP 15640 kb)

Comparison of isotropic and anisotropic representation of 3D STORM localizations

Rotation of a 3D STORM acquired mammalian mitochondria segment (U2OS cell transfected with TOM20-GFP and nanobody label with Alexa 647) to illustrate differences in localization precision between the lateral and axial dimensions using ViSP. The left panel is a reconstruction with isotropic Gaussians, while the right panel is that of a reconstruction with anisotropic Gaussians, revealing a poorer localization precision in the axial (z) dimension. Size of region is 1.4 × 3.2 × 1.8 μm. (MOV 3790 kb)

Cluster segmentation of 3D STORM mammalian mitochondria network

Left panel shows a 200,000 localization reconstruction of a 3D STORM acquired mammalian mitochondria network (U2OS cell transfected with TOM20-GFP and nanobody labeling with Alexa 647). Right panel is a surface rendering and cluster segmentation of the mitochondria after a local density threshold using ViSP. (MOV 27813 kb)

Comparison of localization- and surface-based representation of 3D PALM/STORM multi-channel data

Left panel is a localization-based representation of a multi-channel centrosome complex (mEos2-Centrin1 in red and Alexa 647-labelled Cep 164 in blue) in a combined 3D PALM/STORM acquisition. Right panel is the representation of the same channels using ViSP's surface rendering feature. (MOV 13957 kb)

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Beheiry, M., Dahan, M. ViSP: representing single-particle localizations in three dimensions. Nat Methods 10, 689–690 (2013). https://doi.org/10.1038/nmeth.2566

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