scholarly journals VirusMapper: open-source nanoscale mapping of viral architecture through super-resolution microscopy

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Robert D. M. Gray ◽  
Corina Beerli ◽  
Pedro Matos Pereira ◽  
Kathrin Maria Scherer ◽  
Jerzy Samolej ◽  
...  
Keyword(s):  
Open Source ◽  
Super Resolution ◽  
Super Resolution Microscopy

scholarly journals NanoJ: a high-performance open-source super-resolution microscopy toolbox

2018 ◽  
Author(s):  
Romain F. Laine ◽  
Kalina L. Tosheva ◽  
Nils Gustafsson ◽  
Robert D. M. Gray ◽  
Pedro Almada ◽  
...  
Keyword(s):  
Image Analysis ◽  
Open Source ◽  
High Performance ◽  
Image Quality Assessment ◽  
Fluorescent Microscopy ◽  
Super Resolution ◽  
Quantitative Information ◽  
Ease Of Use ◽  
Source Image ◽  
Super Resolution Microscopy

Super-resolution microscopy has become essential for the study of nanoscale biological processes. This type of imaging often requires the use of specialised image analysis tools to process a large volume of recorded data and extract quantitative information. In recent years, our team has built an open-source image analysis framework for super-resolution microscopy designed to combine high performance and ease of use. We named it NanoJ - a reference to the popular ImageJ software it was de-veloped for. In this paper, we highlight the current capabilities of NanoJ for several essential processing steps: spatio-temporal alignment of raw data (NanoJ-Core), super-resolution image re-construction (NanoJ-SRRF), image quality assessment (NanoJ-SQUIRREL), structural modelling (NanoJ-VirusMapper) and control of the sample environment (NanoJ-Fluidics). We expect to expand NanoJ in the future through the development of new tools designed to improve quantitative data analysis and measure the reliability of fluorescent microscopy studies.

scholarly journals Super-Beacons: open-source probes with spontaneous tuneable blinking compatible with live-cell super-resolution microscopy

2020 ◽  
Author(s):  
Pedro M. Pereira ◽  
Nils Gustafsson ◽  
Mark Marsh ◽  
Musa M. Mhlanga ◽  
Ricardo Henriques
Keyword(s):  
Open Source ◽  
Single Molecule ◽  
High Intensity ◽  
Transmembrane Proteins ◽  
Super Resolution ◽  
Live Cell ◽  
New Class ◽  
High Illumination ◽  
Super Resolution Microscopy

Localization based super-resolution microscopy relies on the detection of individual molecules cycling between fluorescent and non-fluorescent states. These transitions are commonly regulated by high-intensity illumination, imposing constrains to imaging hardware and producing sample photodamage. Here, we propose single-molecule self-quenching as a mechanism to generate spontaneous photoswitching independent of illumination. To demonstrate this principle, we developed a new class of DNA-based open-source Super-Resolution probes named Super-Beacons, with photoswitching kinetics that can be tuned structurally, thermally and chemically. The potential of these probes for live-cell friendly Super-Resolution Microscopy without high-illumination or toxic imaging buffers is revealed by imaging Interferon Inducible Transmembrane proteins (IFITMs) at sub-100nm resolutions.

scholarly journals NanoJ: a high-performance open-source super-resolution microscopy toolbox

2019 ◽  
Vol 52 (16) ◽  
pp. 163001 ◽  
Author(s):  
Romain F Laine ◽  
Kalina L Tosheva ◽  
Nils Gustafsson ◽  
Robert D M Gray ◽  
Pedro Almada ◽  
...  
Keyword(s):  
Open Source ◽  
High Performance ◽  
Super Resolution ◽  
Super Resolution Microscopy

scholarly journals Super‐beacons: Open‐source probes with spontaneous tuneable blinking compatible with live‐cell super‐resolution microscopy

Traffic ◽  
2020 ◽  
Vol 21 (5) ◽  
pp. 375-385
Author(s):  
Pedro M. Pereira ◽  
Nils Gustafsson ◽  
Mark Marsh ◽  
Musa M. Mhlanga ◽  
Ricardo Henriques
Keyword(s):  
Open Source ◽  
Super Resolution ◽  
Live Cell ◽  
Super Resolution Microscopy
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