NanoJ-SQUIRREL

SQUIRREL is an analytical approach for quantifying image quality in super-resolution microscopy, provided as a GPU-enabled open-source ImageJ plugin. SQUIRREL requires two input images - a super-resolution image (or image stack) and the diffraction-limited equivalent of the same imaging volume. It then calculates an error-map, highlighting areas of the super-resolution image which exhibit poor agreement with the diffraction-limited image, and quality metrics for the super-resolution image.

🔗Source-Code Repository

Main publication:

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* Published in Nature methods, April 2018 (see publication) Research themes: New Methods, Software Type: Paper, Corresponding author

Other publications using resource:

Fluctuation-Based Super-Resolution Traction Force Microscopy Aki Stubb, *Romain F Laine*, Camilo Guzmán, *Ricardo Henriques*, Guillaume Jacquemet, Johanna Ivaska Published in Nano Letters, March 2020 (see publication) Research themes: New Methods, Software Type: Paper

Fix your membrane receptor imaging: Actin cytoskeleton and CD4 membrane organization disruption by chemical fixation *Pedro M Pereira*, *David Albrecht*, *Siân Culley*, *Caron Jacobs*, Mark Marsh, Jason Mercer, *Ricardo Henriques* Published in Frontiers in immunology, April 2019 (see publication) Research themes: Cell Signalling, New Methods Type: Paper, Corresponding author

Automating multimodal microscopy with NanoJ-Fluidics *Pedro Almada*, *Pedro M Pereira*, *Siân Culley*, Ghislaine Caillol, Fanny Boroni-Rueda, Christina L Dix, Guillaume Charras, Buzz Baum, *Romain F Laine*, Christophe Leterrier, *Ricardo Henriques* Published in Nature communications, March 2019 (see publication) Research themes: New Methods, Hardware Type: Paper, Corresponding author

NanoJ: a high-performance open-source super-resolution microscopy toolbox *Romain F Laine*, *Kalina L Tosheva*, *Nils Gustafsson*, *Robert DM 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* Published in Journal of Physics D: Applied Physics, February 2019 (see publication) Research themes: New Methods, Software Type: Paper, Corresponding author

Content-aware image restoration: pushing the limits of fluorescence microscopy Martin Weigert, Uwe Schmidt, Tobias Boothe, Andreas Müller, Alexandr Dibrov, Akanksha Jain, Benjamin Wilhelm, Deborah Schmidt, Coleman Broaddus, *Siân Culley*, Mauricio Rocha-Martins, Fabián Segovia-Miranda, Caren Norden, *Ricardo Henriques*, Marino Zerial, Michele Solimena, Jochen Rink, Pavel Tomancak, Loic Royer, Florian Jug, Eugene W Myers Published in Nature methods, December 2018 (see publication) Research themes: New Methods, Software Type: Paper

SRRF: Universal live-cell super-resolution microscopy *Siân Culley*, *Kalina L Tosheva*, *Pedro Matos Pereira*, *Ricardo Henriques* Published in The international journal of biochemistry & cell biology, August 2018 (see publication) Research themes: New Methods, Software Type: Paper, Corresponding author