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Publication: Henriques et al. Nature methods 2010

QuickPALM is an open-source, freely available image processing algorithm developed as a plugin for ImageJ software. It enables real-time 3D reconstruction of super-resolution images obtained through photoactivated localization microscopy (PALM) or stochastic optical reconstruction microscopy (STORM).

The key innovation of QuickPALM is the use of a fast and simple image processing algorithm that achieves near real-time analysis speeds. This is accomplished through a peak detection method based on the Högbom CLEAN algorithm, followed by a center-of-mass approach to determine the x, y, and z coordinates of each detected molecule's point spread function. The axial (z) position is extracted by introducing astigmatism. Together, this streamlined processing pipeline enables analysis speeds on the order of 30-50 ms per frame, matching the acquisition rates of common EMCCD cameras used for PALM/STORM imaging.

Additional features that make QuickPALM a versatile tool include drift correction and real-time acquisition control. Drift during image acquisition can substantially degrade resolution, but QuickPALM corrects for this by tracking fiduciary landmarks like beads to estimate drift in 2D or 3D. The drift is then subtracted from the localized molecule positions. QuickPALM is also fully integrated with the μManager open-source microscope control software, enabling coordinated control of imaging parameters.

The combination of real-time analysis and acquisition control allows QuickPALM to reconstruct super-resolution data as it is collected. This capability critically enables real-time visualization and inspection of PALM/STORM data rather than waiting hours or days. QuickPALM was demonstrated to achieve lateral resolutions around 40 nm and axial resolution around 50 nm over a 1 μm depth when imaging microtubules in neuronal cells labeled with photoswitchable dyes.

QuickPALM helps overcome two main barriers that have limited adoption of PALM/STORM to date: long processing times for image reconstruction and lack of freely available software. By enabling real-time super-resolution imaging on conventional microscopes outfitted for PALM/STORM, QuickPALM makes this powerful technique more accessible. The open-source ImageJ plugin implementation also facilitates community extensions and customization. Altogether, QuickPALM represents an important advance that should substantially expand utilization of super-resolution microscopy approaches.

Publications featuring QuickPALM

vLUME - 3D virtual reality for single-molecule localization microscopy
Alexander Spark, Alexandre Kitching, Daniel Esteban-Ferrer, Anoushka Handa, Alexander R. Carr, Lisa-Maria Needham, Aleks Ponjavic, Ana Mafalda Santos, James McColl, Christophe Leterrier, Simon J. Davis, Ricardo Henriques, Steven F. Lee
Paper published in Nature Methods, October 2020
Technologies: Nuclear-Pores as references, QuickPALM and vLume
Funded by: BBSRC and Wellcome Trust
News: La Razon (ESP), ZAP, Medium US and IEEE Spectrum
Blogs: Qubit, , Tech Explorist and Whats New
DOI: 10.1038/s41592-020-0962-1
An Introduction to Live-Cell Super-Resolution Imaging
Siân Culley, Pedro Matos Pereira, Romain F Laine, Ricardo Henriques
Book chapter published in Imaging from Cells to Animals In Vivo, January 2020
Technologies: CARE, NanoJ, NanoJ-Fluidics, NanoJ-SQUIRREL, NanoJ-SRRF and QuickPALM
DOI: 10.1201/9781315174662-4
Super-resolution fight club - assessment of 2D and 3D single-molecule localization microscopy software
Daniel Sage, Thanh-An Pham, Hazen Babcock, Tomas Lukes, Thomas Pengo, Jerry Chao, Ramraj Velmurugan, Alex Herbert, Anurag Agrawal, Silvia Colabrese, Ann Wheeler, Anna Archetti, Bernd Rieger, Raimund Ober, Guy M. Hagen, Jean-Baptiste Sibarita, Jonas Ries, Ricardo Henriques, Michael Unser, Seamus Holden
Paper published in Nature Methods, April 2019
Technologies: NanoJ-SRRF and QuickPALM
Funded by: BBSRC
DOI: 10.1038/s41592-019-0364-4
NanoJ - a high-performance open-source super-resolution microscopy toolbox
Romain F Laine, Kalina L Tosheva, Nils Gustafsson, Robert D M Gray, Pedro Almada, David Albrecht, Gabriel T Risa, Fredrik Hurtig, Ann-Christin Lindås, Buzz Baum, Jason Mercer, Christophe Leterrier, Pedro M Pereira, Siân Culley, Ricardo Henriques
Paper published in Journal of Physics D - Applied Physics, January 2019
Technologies: NanoJ, NanoJ-Fluidics, NanoJ-SQUIRREL, NanoJ-SRRF, NanoJ-VirusMapper and QuickPALM
Funded by: BBSRC and Wellcome Trust
DOI: 10.1088/1361-6463/ab0261
Quantitative mapping and minimization of super-resolution optical imaging artifacts
Siân Culley, David Albrecht, Caron Jacobs, Pedro Matos Pereira, Christophe Leterrier, Jason Mercer, Ricardo Henriques
Paper published in Nature Methods, February 2018
Technologies: NanoJ, NanoJ-SQUIRREL, NanoJ-SRRF and QuickPALM
Funded by: BBSRC and Wellcome Trust
DOI: 10.1038/nmeth.4605
Fast live-cell conventional fluorophore nanoscopy with ImageJ through super-resolution radial fluctuations
Nils Gustafsson, Siân Culley, George Ashdown, Dylan M. Owen, Pedro Matos Pereira, Ricardo Henriques
Paper published in Nature Communications, August 2016
Technologies: QuickPALM
Funded by: BBSRC
DOI: 10.1038/ncomms12471
Super-resolution microscopy reveals a preformed NEMO lattice structure that is collapsed in incontinentia pigmenti
Janine Scholefield, Ricardo Henriques, Anca F Savulescu, Elisabeth Fontan, Alix Boucharlat, Emmanuel Laplantine, Asma Smahi, Alain Israël, Fabrice Agou, Musa M Mhlanga
Paper published in Nature Communications, January 2016
Technologies: QuickPALM
Funded by: BBSRC
DOI: 10.1038/ncomms12629
PALM and STORM - Into large fields and high-throughput microscopy with sCMOS detectors
Pedro Almada, Siân Culley, Ricardo Henriques
Review published in Methods, January 2015
Technologies: QuickPALM
DOI: 10.1016/j.ymeth.2015.06.004
High-content 3D multicolor super-resolution localization microscopy
Pedro M Pereira, Pedro Almada, Ricardo Henriques
Book chapter published in Methods in cell biology, January 2015
Technologies: QuickPALM
Regulated vesicle fusion generates signaling nanoterritories that control T cell activation at the immunological synapse
Helena Soares, Ricardo Henriques, Martin Sachse, Leandro Ventimiglia, Miguel A Alonso, Christophe Zimmer, Maria-Isabel Thoulouze, Andrés Alcover
Paper published in Journal of Experimental Medicine, January 2013
Technologies: QuickPALM
DOI: 10.1084/jem.20130150
Hierarchies of host factor dynamics at the entry site of Shigella flexneri during host cell invasion
Soudeh Ehsani, José Carlos Santos, Cristina D Rodrigues, Ricardo Henriques, Laurent Audry, Christophe Zimmer, Philippe Sansonetti, Guy Tran Van Nhieu, Jost Enninga
Paper published in Infection and immunity, January 2012
Technologies: QuickPALM
DOI: 10.1128/IAI.06391-11
Single-molecule localization super-resolution microscopy - deeper and faster
Sébastien Herbert, Helena Soares, Christophe Zimmer, Ricardo Henriques
Review published in Microscopy and microanalysis, January 2012
Technologies: QuickPALM
DOI: 10.1017/S1431927612013347
PALM and STORM - unlocking live‐cell super‐resolution
Ricardo Henriques, Caron Griffiths, E Hesper Rego, Musa M Mhlanga
Review published in Biopolymers, January 2011
Technologies: QuickPALM
DOI: 10.1002/bip.21586
QuickPALM - 3D real-time photoactivation nanoscopy image processing in ImageJ
Ricardo Henriques, Mickael Lelek, Eugenio F Fornasiero, Flavia Valtorta, Christophe Zimmer, Musa M Mhlanga
Paper published in Nature methods, January 2010
Technologies: QuickPALM
DOI: 10.1038/nmeth0510-339

Funding contributing to QuickPALM

Sub-cellular Metabolic Compartmentalization During Oocyte Development
Zita Carvalho dos Santos, Ricardo Henriques, Jorge Carvalho
Funded by: CZI - Measuring Metabolism Across Scales
Duration: January 2024 - December 2026
VP-CLEM-KIT - a pipeline for democratising volumetric visual proteomics
Lucy Collinson, Ricardo Henriques, Paul French
Funded by: CZI - Visual Proteomics Imaging
Duration: December 2021 - June 2024
Publications: 11
Enabling Live-Cell 4D Super-Resolution Microscopy Guided by Artificial Intelligence
Ricardo Henriques
Alias: SelfDriving4DSR
Funded by: ERC - Consolidator
Duration: September 2021 - September 2026
Publications: 23
Optial Biology PhD programme
Michael Hausser, Ricardo Henriques, Antonella Riccio
Funded by: Wellcome Trust - 4-year PhD Programme in Science
Duration: August 2021 - August 2025
Unveiling live-cell viral replication at the nanoscale
Ricardo Henriques
Funded by: EMBO - Installation Grant
Duration: January 2021 - January 2026
Publications: 16
Understanding cellular organisation - from archaea to eukaryotes
Buzz Baum, Mohan Balasubramanian, Jan Löwe, Ricardo Henriques, Ann-Christin Lindas, Thijs Ettema, Ethan Garner
Funded by: Wellcome Trust - Collaborative Award in Science
Duration: December 2016 - December 2021
Publications: 28
Super-Beacons and Beacon-STORM - a new generation of small tunable photoswitching probes and Super-Resolution approaches
Ricardo Henriques
Funded by: BBSRC - New Investigator Research Grant
Duration: January 2016 - December 2018
Publications: 24
Understanding virus cell entry
Caron Jacobs
Funded by: UK-SA Commonwealth Commission - PhD Scholarship
Duration: January 2014 - December 2018
Imaging the structure and dynamics of molecules and complexes in living organisms
Nuno Moreno, Adan Guerrero Cardenas, Adriano Henriques, Antonio Jacinto, Beatriz García Fernández, Emilio José Gualda Manzano, Florence Janody, José Feijó, Lars Jansen, Mariana Pinho, Monica Bettencourt Carvalho Dias, Pedro Almada, Raquel Oliveira, Ricardo Henriques, Sérgio Filipe, Susana Gouveia, Teresa Costa
Funded by: FCT - Projectos de IC&DT de Consolidação de Competências e Recursos em Investigação
Duration: July 2013 - December 2016
Enhancing single-molecule localization super-resolution microscopy
Ricardo Henriques
Funded by: Pasteur-Roux-Cantarini - Postdoctoral Fellowships
Duration: January 2012 - August 2013
Spatio-temporal tracking of gene expression in living cells via super-resolution microscopy
Ricardo Henriques
Funded by: FCT - PhD Fellowship
Duration: January 2010 - October 2011
Super-resolution imaging of gene expression and nuclear architecture
Musa Mhlanga, Ricardo Henriques
Funded by: FCT - R&D Projects
Duration: January 2009 - December 2012