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ISTDECO :
ISTDECO : In Situ Transcriptomics Decoding by Deconvolution
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- Andersson, Axel (författare)
- Uppsala universitet,Science for Life Laboratory, SciLifeLab,Bildanalys och människa-datorinteraktion,Avdelningen Vi3
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- Diego, Ferran (författare)
- HCI/IWR and Department of Physics and Astronomy, Heidelberg University, Heidelberg
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- Hamprecht, Fred A. (författare)
- Uppsala universitet,Avdelningen Vi3,Bildanalys och människa-datorinteraktion,Science for Life Laboratory, SciLifeLab,HCI/IWR and Department of Physics and Astronomy, Heidelberg University, Heidelberg
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- Wählby, Carolina, professor, 1974- (författare)
- Uppsala universitet,Bildanalys och människa-datorinteraktion,Science for Life Laboratory, SciLifeLab,Avdelningen Vi3
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(creator_code:org_t)
- Engelska.
- Relaterad länk:
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https://doi.org/10.1...
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https://urn.kb.se/re...
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Abstract
Ämnesord
Stäng
- In Situ Transcriptomics (IST) is a set of image-based transcriptomics approaches that enables localisation of gene expression directly in tissue samples. IST techniques produce multiplexed image series in which fluorescent spots are either present or absent across imaging rounds and colour channels. A spot’spresence and absence form a type of barcoded pattern that labels a particular type of mRNA. Therefore, the expression of agene can be determined by localising the fluorescent spots and decode the barcode that they form. Existing IST algorithms usually do this in two separate steps: spot localisation and barcode decoding. Although these algorithms are efficient, they are limited by strictly separating the localisation and decoding steps. This limitation becomes apparent in regions with low signal-to-noise ratio or high spot densities. We argue that an improved gene expression decoding can be obtained by combining these two steps into a single algorithm. This allows for an efficient decoding that is less sensitive to noise and optical crowding. We present IST Decoding by Deconvolution (ISTDECO), a principled decoding approach combining spectral and spatial deconvolution into a single algorithm. We evaluate ISTDECOon simulated data, as well as on two real IST datasets, and compare with state-of-the-art. ISTDECO achieves state-of-the-art performance despite high spot densities and low signal-to-noise ratios. It is easily implemented and runs efficiently using a GPU.ISTDECO implementation, datasets and demos are available online at: github.com/axanderssonuu/istdeco
Ämnesord
- TEKNIK OCH TEKNOLOGIER -- Medicinteknik -- Medicinsk bildbehandling (hsv//swe)
- ENGINEERING AND TECHNOLOGY -- Medical Engineering -- Medical Image Processing (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
Nyckelord
- Deconvolution
- In situ sequencing
- Decoding
- Image-based spatial transcriptomics
- Computerized Image Processing
- Datoriserad bildbehandling
- Computerized Image Processing
- Datoriserad bildbehandling
Publikations- och innehållstyp
- vet (ämneskategori)
- ovr (ämneskategori)