SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data.
Localization-based super-resolution techniques open the door to unprecedented analysis of molecular organization. This task often involves complex image processing adapted to the specific topology and quality of the image to be analyzed. Here we present a segmentation framework based on Voronoï tessellation constructed from the coordinates of localized molecules, implemented in freely available and open-source SR-Tesseler software. This method allows precise, robust and automatic quantification of protein organization at different scales, from the cellular level down to clusters of a few fluorescent markers. We validated our method on simulated data and on various biological experimental data of proteins labeled with genetically encoded fluorescent proteins or organic fluorophores. In addition to providing insight into complex protein organization, this polygon-based method should serve as a reference for the development of new types of quantifications, as well as for the optimization of existing ones.
Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France.|Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique (CNRS) UMR 5297, Bordeaux, France.|Bordeaux Imaging Center, University of Bordeaux, Bordeaux, France.|Bordeaux Imaging Center, CNRS UMS 3420, Bordeaux, France.|Bordeaux Imaging Center, INSERM US04, Bordeaux, France.
Florian
F
Levet
Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France.|Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique (CNRS) UMR 5297, Bordeaux, France.
Eric
E
Hosy
Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France.|Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique (CNRS) UMR 5297, Bordeaux, France.|Ecole Nationale Supérieure de Biotechnologie, Constantine, Algeria.
Adel
A
Kechkar
Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France.|Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique (CNRS) UMR 5297, Bordeaux, France.|Imagine Optic, Orsay, France.
Corey
C
Butler
Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France.|Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique (CNRS) UMR 5297, Bordeaux, France.
Anne
A
Beghin
Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France.|Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique (CNRS) UMR 5297, Bordeaux, France.|Bordeaux Imaging Center, University of Bordeaux, Bordeaux, France.|Bordeaux Imaging Center, CNRS UMS 3420, Bordeaux, France.|Bordeaux Imaging Center, INSERM US04, Bordeaux, France.
Daniel
D
Choquet
Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France.|Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique (CNRS) UMR 5297, Bordeaux, France.
Jean-Baptiste
JB
Sibarita
D000465:Algorithms; D000818:Animals; D019556:COS Cells; D002522:Chlorocebus aethiops; D016000:Cluster Analysis; D019295:Computational Biology; D003198:Computer Simulation; D005456:Fluorescent Dyes / Q000737:chemistry; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008856:Microscopy, Fluorescence / Q000379:methods*; D009474:Neurons / Q000378:metabolism / Q000502:physiology; D009865:Oocytes / Q000378:metabolism; D010363:Pattern Recognition, Automated; D018009:Receptors, Glycine / Q000378:metabolism*; D012984:Software; D014982:Xenopus laevis
D005456:Fluorescent Dyes; D018009:Receptors, Glycine