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

  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},
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… 

SMAP – A Modular Superresolution Microscopy Analysis Platform for SMLM Data

SMAP is a powerful, ready-to-use software package for all steps of SMLM data analysis, that enables anyone to use state-of-the art algorithms and complex analysis workflows and that provides a versatile platform for developers to share and publish new S MLM algorithms.

SMAP: a modular super-resolution microscopy analysis platform for SMLM data

  • J. Ries
  • Computer Science
    Nature Methods
  • 2020
A modular Super-resolution Microscopy Analysis Platform (SMAP) that integrates all steps of data analysis and is easy to use and extend, and has a freely configurable graphical user interface (GUI) and currently contains more than 200 plugins.

Synergizing superresolution optical fluctuation imaging with single molecule localization microscopy

It is shown that SOFI-assisted SMLM imaging can improve image reconstruction by rejecting common sources of background and by efficient optical sectioning and by shortening image reconstruction time, and could set an example for synergizing additional imaging techniques.

Correlated confocal and super-resolution imaging by VividSTORM

A 5-d tissue processing and immunostaining procedure that is optimized for SMLM, and an open-source software, VividSTORM, which facilitates the measurement of molecular abundance, clustering, internalization, surface density and intermolecular distances in a cell-specific and subcellular compartment–restricted manner.

Image artifacts in Single Molecule Localization Microscopy: why optimization of sample preparation protocols matters

Three well-optimized fixation protocols for staining microtubules, mitochondria and actin in a mammalian cell line are presented and various artifacts in relation to images obtained from samples prepared using the protocols are discussed.

Elements of image processing in localization microscopy

The usefulness of image simulations as a guide to the potential artefacts that can arise when processing over-dense experimental fluorescence images with a sparse localization algorithm are demonstrated.

Superresolution microscope image reconstruction by spatiotemporal object decomposition and association: application in resolving t-tubule structure in skeletal muscle.

A new image reconstruction algorithm based on tracklets, short trajectories of the same objects, which is able to resolve low to medium density of overlapping emitters with improved localization accuracy and resolves the transverse tubule structure of the mammalian skeletal muscle for the first time.

Teaching deep neural networks to localize single molecules for super-resolution microscopy

This work presents a novel localization algorithm based on deep learning which significantly improves upon the state of the art on the SMLM2016 challenge, and investigates how unsupervised learning can be used to make the network robust against mismatch between simulated and real data.

Teaching deep neural networks to localize sources in super-resolution microscopy by combining simulation-based learning and unsupervised learning

A novel localization algorithm based on deep learning which significantly improves upon the state of the art and enables faster imaging than previous approaches and more generally shows how to train deep networks to solve challenging Bayesian inverse problems in biology and physics.

A three-camera imaging microscope for high-speed single-molecule tracking and super-resolution imaging in living cells

A three-camera imaging microscope for fast tracking of multiple interacting molecules simultaneously, with high spatiotemporal resolution, to develop quantitative single-molecule assays to study when and where molecules are interacting inside living cells and where enzymes are active.



Widely accessible method for superresolution fluorescence imaging of living systems

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

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.

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)

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

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)

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.

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

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.