ArticleNature methods2024
Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- HIT-MAP: A scalable approach to multimodal mapping of subcellular organization.Cell reports methods · 2026Article
- Time-resolved phenotyping at subcellular resolution reveals shared principles and key trade-offs across antimicrobial peptide activities.bioRxiv : the preprint server for biology · 2026Article
- The Wiskott-Aldrich Syndrome protein (WASp) contribution to microglial phagocytic function and neurodevelopmental support.Journal of neuroinflammation · 2026Article
- Imaging-Based Spatial Transcriptomics: Data Interpretation Methods and Biomedical Applications.Biology · 2026Review
- Chromatin-associated intronic RNAs from long genes form introsomes that shape nuclear architecture in neuronal cells.bioRxiv : the preprint server for biology · 2026Article
- Image Tracing of Inflammatory Intestinal Organoids via Computational Clearing.Nanomaterials (Basel, Switzerland) · 2026Article
- GPSeq maps the radial organization of eukaryotic genomes along the nuclear periphery-center axis.Nature protocols · 2026Review
- Actomyosin contractility drives apical polarization and membrane transport during tubulogenesis.Research square · 2026Article
- Phase-based computational adaptive optics enables artifact-free super-resolution microscopy.Communications engineering · 2026Article
- A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest.Genome research · 2026Review
- A Multimodal Single-Cell Epigenomic and 3D Genome Atlas of the Human Basal Ganglia.bioRxiv : the preprint server for biology · 2026Article
- Point spread function decoupling in computational fluorescence microscopy.Light, science & applications · 2026Article
- Depth-variant deconvolution applied to widefield microscopy for rapid large-volume tissue imaging.Communications biology · 2025Article
- High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer.Science (New York, N.Y.) · 2025Article
- Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression.Nature methods · 2025Article
- Best practices in plant fluorescence imaging and reporting: A primer.The Plant cell · 2025Review
- Coding principles of dopaminergic transmission modes.Science advances · 2025Article
- Enhancing ultra-high density single-molecule localization with deep spatiotemporal networks.Biomedical optics express · 2025Article
- Computational Super-Resolution: An Odyssey in Harnessing Priors to Enhance Optical Microscopy Resolution.Analytical chemistry · 2025Review
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17 authors.
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Abstract
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 ×20 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.
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