Analyzing and quantifying single-molecule localization microscopy data [NEUBIAS Academy@Home]Webinar
Channel: NEUBIAS
Date: 2020-06-18

After watching the first part of this webinar, by Siân Culley, attendees should be to choose the most appropriate methods for localizing molecules in raw SMLM data and quantifying these localizations. They should also be able to properly interpret their quantifications by having knowledge of the common pitfalls encountered in SMLM.
In the second part Florian Levet speaks about SR-Tesseler, an open-source and interactive software platform that allows multiscale segmention and quantification of 2D localization microscopy data. He also unveils new possibilities for 3D segmentation and analysis in SR-Tesseler.

Part 1: Basic SMLM analysis
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00:01:27   Basic overview of SMLM and analysis
00:07:00   Introduction to ThunderSTORM software
00:10:25   High and low density
00:12:11   Demo: ThunderSTORM on sparse data
00:31:03   Analysis problems with high density data
00:35:05   Demo: ThunderSTORM on high density data
00:38:52   Alternative methods for high density data
00:41:58   Artefacts in SMLM analysis
00:45:05   Demo: Quality assessment with SQUIRREL
00:47:24   Localization in the axial direction
00:48:44   Demo: ThunderSTORM on astigmatism data
00:53:23   Wrap-up of SMLM analysis and Q&A
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Part 2: Quantifying SMLM data
01:00:33   Overview of part 2
01:01:33   Introduction to rendering and quantification methods
01:05:44   Ripley’s functions for cluster analysis
01:09:52   Pair correlation cluster analysis
01:10:54   Bayesian cluster analysis
01:12:16   Machine learning-based cluster analysis
01:13:40   DBSCAN segmentation analysis
01:16:17   Tesselation-based techniques (SR-TESSELER)
01:23:03   Quantifying segmented objects
01:24:49   3D segmentation methods
01:26:07   Molecule counting and stoichiometry
01:29:17   Ratiometric quantification
01:32:20   Stoichiometric quantification with qPAINT
01:35:34   Demo: SR-TESSELER
01:42:11   Q&A

Slides available at
- https://github.com/superresolusian/NEUBIAS-webinar
- https://github.com/flevet/NEUBIAS_Academy/blob/master/2020_06_11_SMLM_quantification_NEUBIAS_Academy.pdf
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Presenters

Siân Culley, Postdoc at UCL, London, UK.
Florian Levet, Researcher at IINS, Bordeaux, France

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Moderators

Bram van den Broek, Netherlands Cancer Institute, Amsterdam, NL
Daniel Sage, EPFL, Lausanne, Switserland
Pedro Matos-Perreira, ITQB, Lison, Portugal

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All Questions & Answers will available on the image.sc forum, where you can further ask questions in the future:
https://forum.image.sc/t/neubias-academy-home-webinar-analyzing-and-quantifying-single-molecule-localization-microscopy-data-questions-answers/39591

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