Technology
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
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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 and QuickPALM DOI: 10.1201/9781315174662-4 |
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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, January 2020 Technologies: Nuclear-Pores as references, QuickPALM and vLume Funded by: BBSRC and Wellcome Trust News: Technology Networks, La Razon (ESP), ZAP and Medium US Blogs: Qubit, , Tech Explorist and Whats New DOI: 10.1038/s41592-020-0962-1 |
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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: CARE, NanoJ, NanoJ-Fluidics, NanoJ-SQUIRREL, NanoJ-SRRF, NanoJ-VirusMapper and QuickPALM Funded by: BBSRC and Wellcome Trust DOI: 10.1088/1361-6463/ab0261 |
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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, January 2019 Technologies: QuickPALM Funded by: BBSRC DOI: 10.1038/s41592-019-0364-4 |
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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, January 2018 Technologies: NanoJ, NanoJ-SQUIRREL and QuickPALM Funded by: BBSRC and Wellcome Trust News: physicsworld.com DOI: 10.1038/nmeth.4605 |
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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, January 2016 Technologies: NanoJ-SRRF and QuickPALM Funded by: BBSRC News: Azom.com DOI: 10.1038/ncomms12471 |
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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 and FCT DOI: 10.1038/ncomms12629 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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Funding contributing to QuickPALM
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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 |
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How does membrane topology influence T-cell activation and HIV infection? Simao Coelho Funded by: FCT - Exploratory Research Projects Duration: March 2023 - September 2024 |
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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: 13 |
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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: 28 |
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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 |
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Unveiling live-cell viral replication at the nanoscale Ricardo Henriques Funded by: EMBO - Installation Grant Duration: January 2021 - January 2026 Publications: 21 |
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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 |
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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 |
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Understanding virus cell entry Caron Jacobs Funded by: UK-SA Commonwealth Commission - PhD Scholarship Duration: January 2014 - December 2018 |
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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 |
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Enhancing single-molecule localization super-resolution microscopy Ricardo Henriques Funded by: Pasteur-Roux-Cantarini - Postdoctoral Fellowships Duration: January 2012 - August 2013 |
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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 |
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Super-resolution imaging of gene expression and nuclear architecture Musa Mhlanga, Ricardo Henriques Funded by: FCT - R&D Projects Duration: January 2009 - December 2012 Publications: 1 |