Localizer: fast, accurate, open-source, and modular software package for superresolution microscopy

@article{Dedecker2012LocalizerFA,
  title={Localizer: fast, accurate, open-source, and modular software package for superresolution microscopy},
  author={Peter Dedecker and Sam Duw{\'e} and Robert K. Neely and Jin Zhang},
  journal={Journal of Biomedical Optics},
  year={2012},
  volume={17}
}
Abstract. We present Localizer, a freely available and open source software package that implements the computational data processing inherent to several types of superresolution fluorescence imaging, such as localization (PALM/STORM/GSDIM) and fluctuation imaging (SOFI/pcSOFI). Localizer delivers high accuracy and performance and comes with a fully featured and easy-to-use graphical user interface but is also designed to be integrated in higher-level analysis environments. Due to its modular… 

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References

SHOWING 1-10 OF 20 REFERENCES

Widely accessible method for superresolution fluorescence imaging of living systems

TLDR
This method, which uses off-the-shelf equipment, genetically encodable labels, and simple and rapid data acquisition, is capable of providing two- to threefold-enhanced spatial resolution, significant background rejection, markedly improved contrast, and favorable temporal resolution in living cells.

Real‐time computation of subdiffraction‐resolution fluorescence images

TLDR
It is found that real‐time data processing is possible and that super‐resolution imaging with organic fluorophores of cellular structures with ∼20 nm optical resolution can be completed in less than 10 s.

Ultra-high resolution imaging by fluorescence photoactivation localization microscopy.

TLDR
A new method for fluorescence imaging has been developed that can obtain spatial distributions of large numbers of fluorescent molecules on length scales shorter than the classical diffraction limit, and suggests a means to address a significant number of biological questions that had previously been limited by microscope resolution.

Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI)

TLDR
This work presents an approach for obtaining subdiffraction limit optical resolution in all three dimensions, and demonstrates a 5-fold improvement in spatial resolution by using a conventional wide-field microscope.

Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes

TLDR
An analytical single-particle tracking method and tool, multiple-target tracing (MTT), that takes advantage of the high spatial resolution provided by single-fluorophore sensitivity to generate dynamic maps at high densities of tracked particles, thereby providing global representation of molecular dynamics in cell membranes.

Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)

TLDR
A high-resolution fluorescence microscopy method based on high-accuracy localization of photoswitchable fluorophores that can, in principle, reach molecular-scale resolution is developed.

QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ

To the Editor: Although conventional microscopes have a reso-lution limited by diffraction to about half the wavelength of light, several recent advances have led to microscopy methods that achieve

Binding-activated localization microscopy of DNA structures.

TLDR
The principle of binding-activated localization microscopy (BALM) can be extended to other dyes and targets such as protein structures and is applied to visualize the organization of the bacterial chromosome in fixed Escherichia coli cells.

Imaging Intracellular Fluorescent Proteins at Nanometer Resolution

TLDR
This work introduced a method for optically imaging intracellular proteins at nanometer spatial resolution and used this method to image specific target proteins in thin sections of lysosomes and mitochondria and in fixed whole cells to image retroviral protein Gag at the plasma membrane.