Simulations of camera-based single-molecule fluorescence experiments.
Single-molecule microscopy has become a widely used technique in (bio)physics and (bio)chemistry. A popular implementation is single-molecule Förster Resonance Energy Transfer (smFRET), for which total internal reflection fluorescence microscopy is frequently combined with camera-based detection of...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2018-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5898730?pdf=render |
| _version_ | 1818142362361135104 |
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| author | Richard Börner Danny Kowerko Mélodie C A S Hadzic Sebastian L B König Marc Ritter Roland K O Sigel |
| author_facet | Richard Börner Danny Kowerko Mélodie C A S Hadzic Sebastian L B König Marc Ritter Roland K O Sigel |
| author_sort | Richard Börner |
| collection | DOAJ |
| description | Single-molecule microscopy has become a widely used technique in (bio)physics and (bio)chemistry. A popular implementation is single-molecule Förster Resonance Energy Transfer (smFRET), for which total internal reflection fluorescence microscopy is frequently combined with camera-based detection of surface-immobilized molecules. Camera-based smFRET experiments generate large and complex datasets and several methods for video processing and analysis have been reported. As these algorithms often address similar aspects in video analysis, there is a growing need for standardized comparison. Here, we present a Matlab-based software (MASH-FRET) that allows for the simulation of camera-based smFRET videos, yielding standardized data sets suitable for benchmarking video processing algorithms. The software permits to vary parameters that are relevant in cameras-based smFRET, such as video quality, and the properties of the system under study. Experimental noise is modeled taking into account photon statistics and camera noise. Finally, we survey how video test sets should be designed to evaluate currently available data analysis strategies in camera-based sm fluorescence experiments. We complement our study by pre-optimizing and evaluating spot detection algorithms using our simulated video test sets. |
| first_indexed | 2024-12-11T11:14:34Z |
| format | Article |
| id | doaj.art-6dd5421c76f74e5e9d52150e9eee4b2a |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-11T11:14:34Z |
| publishDate | 2018-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-6dd5421c76f74e5e9d52150e9eee4b2a2022-12-22T01:09:24ZengPublic Library of Science (PLoS)PLoS ONE1932-62032018-01-01134e019527710.1371/journal.pone.0195277Simulations of camera-based single-molecule fluorescence experiments.Richard BörnerDanny KowerkoMélodie C A S HadzicSebastian L B KönigMarc RitterRoland K O SigelSingle-molecule microscopy has become a widely used technique in (bio)physics and (bio)chemistry. A popular implementation is single-molecule Förster Resonance Energy Transfer (smFRET), for which total internal reflection fluorescence microscopy is frequently combined with camera-based detection of surface-immobilized molecules. Camera-based smFRET experiments generate large and complex datasets and several methods for video processing and analysis have been reported. As these algorithms often address similar aspects in video analysis, there is a growing need for standardized comparison. Here, we present a Matlab-based software (MASH-FRET) that allows for the simulation of camera-based smFRET videos, yielding standardized data sets suitable for benchmarking video processing algorithms. The software permits to vary parameters that are relevant in cameras-based smFRET, such as video quality, and the properties of the system under study. Experimental noise is modeled taking into account photon statistics and camera noise. Finally, we survey how video test sets should be designed to evaluate currently available data analysis strategies in camera-based sm fluorescence experiments. We complement our study by pre-optimizing and evaluating spot detection algorithms using our simulated video test sets.http://europepmc.org/articles/PMC5898730?pdf=render |
| spellingShingle | Richard Börner Danny Kowerko Mélodie C A S Hadzic Sebastian L B König Marc Ritter Roland K O Sigel Simulations of camera-based single-molecule fluorescence experiments. PLoS ONE |
| title | Simulations of camera-based single-molecule fluorescence experiments. |
| title_full | Simulations of camera-based single-molecule fluorescence experiments. |
| title_fullStr | Simulations of camera-based single-molecule fluorescence experiments. |
| title_full_unstemmed | Simulations of camera-based single-molecule fluorescence experiments. |
| title_short | Simulations of camera-based single-molecule fluorescence experiments. |
| title_sort | simulations of camera based single molecule fluorescence experiments |
| url | http://europepmc.org/articles/PMC5898730?pdf=render |
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