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3D Single Molecule Localization Microscopy: Key Outcomes of the Software Benchmarking

D. Sage, T.-A. Pham, M. Unser

Proceedings of the Sixteenth IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI'19), Venice, Italian Republic, April 8-11, 2019, pp. 610.



With the large diffusion of the super-resolution localization microscopy technique, a large number of software packages have been developed to accurately localize blinking fluorescent emitters in frames. To guide developers of software and practitioners on their critical choice of software, we have designed a large-scale software benchmarks, first in 2D and very recently in 3D. The 3D setting is challenging computational task because the axial information is encoded by the shape of PSF in 2D images. Our framework is based on 1) the simulation of 3D highly-realistic datasets in the most used 3D modalities, astigmatism (AS), double helix (DH), biplane (BP), 2) the definition of common metrics, and 3) thanks to the involvement of many groups of researchers we have the localization results of more than 30 software on the same datasets. This provides a unique board assessment of the 3D SMLM software and a holistic view of the performances of the 3D software. The complete method and material is available at http://bigwww.epfl.ch/smlm/.


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