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Deconwolf enables h...
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Wernersson, Erik
(author)
Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images
- Article/chapterEnglish2024
Publisher, publication year, extent ...
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2024
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2024
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printrdacarrier
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LIBRIS-ID:oai:DiVA.org:su-231208
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https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-231208URI
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https://doi.org/10.1038/s41592-024-02294-7DOI
Supplementary language notes
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Language:English
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Summary in:English
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Subject category:ref swepub-contenttype
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Subject category:art swepub-publicationtype
Notes
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Microscopy-based spatially resolved omic methods are transforming the life sciences. However, these methods rely on high numerical aperture objectives and cannot resolve crowded molecular targets, limiting the amount of extractable biological information. To overcome these limitations, here we develop Deconwolf, an open-source, user-friendly software for high-performance deconvolution of widefield fluorescence microscopy images, which efficiently runs on laptop computers. Deconwolf enables accurate quantification of crowded diffraction limited fluorescence dots in DNA and RNA fluorescence in situ hybridization images and allows robust detection of individual transcripts in tissue sections imaged with x20 air objectives. Deconvolution of in situ spatial transcriptomics images with Deconwolf increased the number of transcripts identified more than threefold, while the application of Deconwolf to images obtained by fluorescence in situ sequencing of barcoded Oligopaint probes drastically improved chromosome tracing. Deconwolf greatly facilitates the use of deconvolution in many bioimaging applications. Deconwolf is a computationally efficient and user-friendly software tool for fluorescence microscopy image deconvolution that improves the analysis of diverse fluorescence in situ hybridization methods and can handle large datasets.
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Gelali, Eleni
(author)
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Girelli, Gabriele
(author)
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Wang, Su
(author)
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Castillo, David
(author)
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Mattsson Langseth, Christoffer,1994-Stockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab)(Swepub:su)chma0486
(author)
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Verron, Quentin
(author)
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Nguyen, Huy Q.
(author)
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Chattoraj, Shyamtanu
(author)
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Martinez Casals, Anna
(author)
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Blom, Hans
(author)
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Lundberg, Emma
(author)
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Nilsson, Mats,1969-Stockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab)(Swepub:su)matsn
(author)
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Marti-Renom, Marc A.
(author)
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Wu, Chao-ting
(author)
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Crosetto, Nicola
(author)
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Bienko, Magda
(author)
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Stockholms universitetInstitutionen för biokemi och biofysik
(creator_code:org_t)
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In:Nature Methods1548-70911548-7105
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Wernersson, Erik
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Gelali, Eleni
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Girelli, Gabriel ...
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Wang, Su
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Castillo, David
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Mattsson Langset ...
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Verron, Quentin
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Nguyen, Huy Q.
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Chattoraj, Shyam ...
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Martinez Casals, ...
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Blom, Hans
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Lundberg, Emma
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Nilsson, Mats, 1 ...
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Marti-Renom, Mar ...
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Wu, Chao-ting
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Crosetto, Nicola
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Bienko, Magda
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- NATURAL SCIENCES
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NATURAL SCIENCES
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Nature Methods
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Stockholm University