RegiSTORM: channel registration for multi-color stochastic optical reconstruction microscopy

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ovrebo, OysteinImperial Coll London, Dept Mat, London SW7 2AZ, England.;Imperial Coll London, Dept Bioengn, London SW7 2AZ, England.;Imperial Coll London, Inst Biomed Engn, London SW7 2AZ, England. (författare)

RegiSTORM : channel registration for multi-color stochastic optical reconstruction microscopy

Artikel/kapitelEngelska2023

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BMC,2023
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LIBRIS-ID:oai:DiVA.org:uu-506972
https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-506972URI
https://doi.org/10.1186/s12859-023-05320-1DOI
http://kipublications.ki.se/Default.aspx?queryparsed=id:152934616URI

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Språk:engelska
Sammanfattning på:engelska

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Background: Stochastic optical reconstruction microscopy (STORM), a super-resolution microscopy technique based on single-molecule localizations, has become popular to characterize sub-diffraction limit targets. However, due to lengthy image acquisition, STORM recordings are prone to sample drift. Existing cross-correlation or fiducial marker-based algorithms allow correcting the drift within each channel, but misalignment between channels remains due to interchannel drift accumulating during sequential channel acquisition. This is a major drawback in multi-color STORM, a technique of utmost importance for the characterization of various biological interactions.Results: We developed RegiSTORM, a software for reducing channel misalignment by accurately registering STORM channels utilizing fiducial markers in the sample. RegiSTORM identifies fiducials from the STORM localization data based on their non-blinking nature and uses them as landmarks for channel registration. We first demonstrated accurate registration on recordings of fiducials only, as evidenced by significantly reduced target registration error with all the tested channel combinations. Next, we validated the performance in a more practically relevant setup on cells multi-stained for tubulin. Finally, we showed that RegiSTORM successfully registers two-color STORM recordings of cargo-loaded lipid nanoparticles without fiducials, demonstrating the broader applicability of this software.Conclusions: The developed RegiSTORM software was demonstrated to be able to accurately register multiple STORM channels and is freely available as open-source (MIT license) at https://github.com/oystein676/RegiSTORM.git and https://doi.org/10.5281/ zenodo.5509861 (archived), and runs as a standalone executable (Windows) or via Python (Mac OS, Linux).

Ämnesord och genrebeteckningar

NATURVETENSKAP Data- och informationsvetenskap Datorseende och robotik hsv//swe
NATURAL SCIENCES Computer and Information Sciences Computer Vision and Robotics hsv//eng
Super-resolution microscopy
Stochastic optical reconstruction microscopy
Single-molecule localization microscopy
Registration
Multi-channel
Image analysis tool
Software

Biuppslag (personer, institutioner, konferenser, titlar ...)

Ojansivu, MiinaKarolinska Inst, Dept Med Biochem & Biophys, S-17177 Stockholm, Sweden. (författare)
Kartasalo, KimmoKarolinska Inst, Dept Med Epidemiol & Biostat, S-17177 Stockholm, Sweden. (författare)
Barriga, Hanna M. G.Karolinska Inst, Dept Med Biochem & Biophys, S-17177 Stockholm, Sweden. (författare)
Ranefall, Petter,1968-Uppsala universitet,Bildanalys och människa-datorinteraktion,Science for Life Laboratory, SciLifeLab(Swepub:uu)peran517 (författare)
Holme, Margaret N.Karolinska Inst, Dept Med Biochem & Biophys, S-17177 Stockholm, Sweden. (författare)
Stevens, Molly M.Imperial Coll London, Dept Mat, London SW7 2AZ, England.;Imperial Coll London, Dept Bioengn, London SW7 2AZ, England.;Imperial Coll London, Inst Biomed Engn, London SW7 2AZ, England.;Karolinska Inst, Dept Med Biochem & Biophys, S-17177 Stockholm, Sweden. (författare)
Imperial Coll London, Dept Mat, London SW7 2AZ, England.;Imperial Coll London, Dept Bioengn, London SW7 2AZ, England.;Imperial Coll London, Inst Biomed Engn, London SW7 2AZ, England.Karolinska Inst, Dept Med Biochem & Biophys, S-17177 Stockholm, Sweden. (creator_code:org_t)

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Ingår i:BMC Bioinformatics: BMC24:11471-2105

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Av författaren/redakt...: ovrebo, Oystein; Ojansivu, Miina; Kartasalo, Kimmo; Barriga, Hanna M ...; Ranefall, Petter ...; Holme, Margaret ...; visa fler...; Stevens, Molly M ...; visa färre...

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