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Kolmodin Dahlberg, SimonORCID iD iconorcid.org/0009-0004-1327-5721
Publications (2 of 2) Show all publications
Kolmodin Dahlberg, S., Fernandez Bonet, D., Franzén, L., Ståhl, P. & Hoffecker, I. T. (2025). Hidden network preserved in Slide-tags data allows reference-free spatial reconstruction. Nature Communications, 16(1), Article ID 9652.
Open this publication in new window or tab >>Hidden network preserved in Slide-tags data allows reference-free spatial reconstruction
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2025 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 16, no 1, article id 9652Article in journal (Refereed) Published
Abstract [en]

Spatial transcriptomics technologies aim to spatially map gene expression in tissues and typically use oligonucleotide array surfaces that have undergone spatial indexing. These arrays are used to capture nucleic acids diffusing from adjacently placed tissues, allowing subsequent sequencing to reveal both gene and position. Slide-tags is a recently developed method by Russell et al. that inverts this principle. Instead of capturing molecules released from the tissue, probes are detached from a pre-decoded bead array and diffused into tissues, tagging nuclei with spatial barcodes. In this work we reanalyze this data and discover a latent, spatially informative cell-bead network formed incidentally from barcode diffusion and the biophysical properties of the tissue. This allows us to treat Slide-tags as a network-based imaging-by-sequencing approach. By optimizing spatial constraints encoded in the cell-bead network structure, we can achieve unassisted tissue reconstruction, a fundamental shift from classical spatial technologies based on pre-indexed arrays.

Place, publisher, year, edition, pages
Springer Nature, 2025
National Category
Biophysics
Identifiers
urn:nbn:se:kth:diva-372885 (URN)10.1038/s41467-025-65295-w (DOI)001606917700035 ()41173855 (PubMedID)2-s2.0-105020637200 (Scopus ID)
Note

QC 20251114

Available from: 2025-11-14 Created: 2025-11-14 Last updated: 2025-11-14Bibliographically approved
Kolmodin Dahlberg, S. & Hoffecker, I. T. (2023). Developing a method for protein-based DNA microscopy. European Biophysics Journal, 52(SUPPL 1), S190-S190
Open this publication in new window or tab >>Developing a method for protein-based DNA microscopy
2023 (English)In: European Biophysics Journal, ISSN 0175-7571, E-ISSN 1432-1017, Vol. 52, no SUPPL 1, p. S190-S190Article in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
SPRINGER, 2023
National Category
Biophysics
Identifiers
urn:nbn:se:kth:diva-335865 (URN)001029235400655 ()
Note

QC 20230911

Available from: 2023-09-11 Created: 2023-09-11 Last updated: 2025-02-20Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0009-0004-1327-5721

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