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DOI: 10.4121/e0d424e4-5833-4729-a5a0-48ce94ed3f16

Berrevoets, Enya S.; Kessler, Laurell F.; Balakrishnan, Ashwin; Okuda, Ellen Kazumi; Müller-McNicoll, Michaela et. al. (2025): Software for "Smart 3D super-resolution microscopy reveals the architecture of the RNA scaffold in a nuclear body". Version 1. 4TU.ResearchData. software. https://doi.org/10.4121/e0d424e4-5833-4729-a5a0-48ce94ed3f16.v1

Categories

• Biochemistry and Cell Biology
• Biological Sciences

Keywords

Architectural RNA Morphological Sorting NEAT1 Paraspeckle Polarization Analysis Smart Microscopy Spherical Harmonics STED Super-Resolution Microscopy

Licence

Apache-2.0

Interoperability

• RO-Crate Metadata

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by Enya S. Berrevoets , Laurell F. Kessler, Ashwin Balakrishnan , Ellen Kazumi Okuda, Michaela Müller-McNicoll , Mike Heilemann , Bernd Rieger , Sjoerd Stallinga

This software repository contains the code accompanying the paper "Smart 3D super-resolution microscopy reveals the architecture of the RNA scaffold in a nuclear body". The repository includes a python algorithm to automatically detect and image paraspeckles using an Abberior STED microscope, as well as Matlab code to rotationally and translationally align the resulting paraspeckle images and perform shape and polarity analyses on them.

History

• 2025-10-01 first online, published, posted

Publisher

4TU.ResearchData

Format

documentation/.md; script/.py; script/.m; image/.tiff

Associated peer-reviewed publication

Smart 3D super-resolution microscopy reveals the architecture of the RNA scaffold in a nuclear body

References

• https://gitlab.tudelft.nl/E.S.Berrevoets/paraspeckles

Code hosting project url

https://gitlab.tudelft.nl/E.S.Berrevoets/paraspeckles

Data link

https://doi.org/10.5281/zenodo.14179108

Funding

• Gravitation programme IMAGINE! Netherlands Organization for Scientific Research (NWO)
• Deutsche Forschungsgemeinschaft grant CRC 1177 Deutsche Forschungsgemeinschaft
• SubCellular Architecture of LifE (SCALE) consortium Goethe University Frankfurt

Organizations

Department of Imaging Physics, Faculty of Applied Sciences, Delft University of Technology;
Institute of Physical and Theoretical Chemistry, Goethe University;
Institute of Molecular Biosciences, Goethe University;
IMPRS on Cellular Biophysics;
Max Planck Institute for Biophysics