Image analysis

Software for super-resolution fluorescence microscopy

Software has been crucial to super-resolution microscopy since the beginning of the field, and we have a longstanding interest in pushing the limits of single molecule methods, especially STORM/ PALM super-resolution microscopy and single molecule tracking, by developing new single molecule image analysis tools.

Current/ recent software

We host our code on GitHub, you can find it here: https://github.com/HoldenLab

Older software

  • AutoLase (Micromanager plugin), Automatic closed loop control of density of photoactive molecules during PALM experiments.
  • DAOSTORM, multi-emitter fitting for STORM/ PALM.
  • TwoTone, single molecule FRET data analysis software.

People

References

2022

  1. High-resolution imaging of bacterial spatial organization with vertical cell imaging by nanostructured immobilization (VerCINI)
    Kevin D Whitley, Stuart Middlemiss, Calum Jukes, and 2 more authors
    Nature Protocols, 2022
    HTML
  2. DeepBacs for multi-task bacterial image analysis using open-source deep learning approaches
    Christoph Spahn, Estibaliz Gómez-de-Mariscal, Romain F Laine, and 8 more authors
    Communications Biology, 2022
    HTML

2021

  1. Democratising deep learning for microscopy with ZeroCostDL4Mic
    Lucas Chamier, Romain F Laine, Johanna Jukkala, and 8 more authors
    Nature communications, 2021
    HTML

2020

  1. Virtual-SMLM, a virtual environment for real-time interactive SMLM acquisition
    J Griffié, TA Pham, C Sieben, and 6 more authors
    bioRxiv, 2020
    HTML

2019

  1. Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software
    Daniel Sage, Thanh-An Pham, Hazen Babcock, and 8 more authors
    Nature methods, 2019
    HTML

2015

  1. PALMsiever: a tool to turn raw data into results for single-molecule localization microscopy
    Thomas Pengo, Seamus J Holden, and Suliana Manley
    Bioinformatics, 2015
    HTML

2014

  1. 3D high-density localization microscopy using hybrid astigmatic/biplane imaging and sparse image reconstruction
    Junhong Min, Seamus J Holden, Lina Carlini, and 3 more authors
    Biomedical optics express, 2014
    HTML

2011

  1. DAOSTORM: an algorithm for high-density super-resolution microscopy
    Seamus J Holden, Stephan Uphoff, and Achillefs N Kapanidis
    Nature Methods, 2011
    HTML
  2. Identifying molecular dynamics in single-molecule FRET experiments with burst variance analysis
    Joseph P Torella, Seamus J Holden, Yusdi Santoso, and 2 more authors
    Biophysical journal, 2011
    HTML

2010

  1. Defining the Limits of Single-Molecule FRET Resolution in TIRF Microscopy
    Seamus J Holden, Stephan Uphoff, Johannes Hohlbein, and 4 more authors
    Biophysical Journal, 2010
    HTML