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Spage2vec: Unsupervised representation of localized spatial gene expression signatures

The FEBS journal, 2021-03, Vol.288 (6), p.1859-1870

2021

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Automated Training of Deep Convolutional Neural Networks for Cell Segmentation

Scientific reports, 2017-08, Vol.7 (1), p.7860-7, Article 7860

2017

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In situ sequencing for RNA analysis in preserved tissue and cells

Nature methods, 2013-09, Vol.10 (9), p.857-860

2013

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Introducing Hann windows for reducing edge-effects in patch-based image segmentation

PloS one, 2020-03, Vol.15 (3), p.e0229839

2020

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TissUUmaps: interactive visualization of large-scale spatial gene expression and tissue morphology data

Bioinformatics, 2020-08, Vol.36 (15), p.4363-4365

2020

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The quest for multiplexed spatially resolved transcriptional profiling

Nature methods, 2016-07, Vol.13 (8), p.623-624

Wählby, Carolina

2016

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Deep Learning in Image Cytometry: A Review

Cytometry. Part A, 2019-04, Vol.95 (4), p.366-380

2019

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De novo spatiotemporal modelling of cell-type signatures in the developmental human heart using graph convolutional neural networks

PLoS computational biology, 2022-08, Vol.18 (8), p.e1010366

2022

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Label-free deep learning-based species classification of bacteria imaged by phase-contrast microscopy

PLoS computational biology, 2023-11, Vol.19 (11), p.e1011181-e1011181

2023

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Points2Regions: Fast, interactive clustering of imaging-based spatial transcriptomics data

Cytometry. Part A, 2024-07, Vol.105 (9), p.677-687

2024

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PACMan: A software package for automated single‐cell chlorophyll fluorometry

Cytometry. Part A, 2024-03, Vol.105 (3), p.203-213

2024

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TEM image restoration from fast image streams

PloS one, 2021-02, Vol.16 (2), p.e0246336-e0246336

2021

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Genes in human obesity loci are causal obesity genes in C. elegans

PLoS genetics, 2021-09, Vol.17 (9), p.e1009736-e1009736

2021

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Regular Use of Depot Medroxyprogesterone Acetate Causes Thinning of the Superficial Lining and Apical Distribution of Human Immunodeficiency Virus Target Cells in the Human Ectocervix

The Journal of infectious diseases, 2022-04, Vol.225 (7), p.1151-1161

2022

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Automated identification of the mouse brain's spatial compartments from in situ sequencing data

BMC biology, 2020-10, Vol.18 (1), p.144-144, Article 144

2020

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Bridging Histology and Bioinformatics-Computational Analysis of Spatially Resolved Transcriptomics

Proceedings of the IEEE, 2017, Vol.105 (3), p.530-541

2017

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Fully automated cellular-resolution vertebrate screening platform with parallel animal processing

Lab on a chip, 2012-01, Vol.12 (4), p.711-716

2012

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SimSearch: A Human-in-The-Loop Learning Framework for Fast Detection of Regions of Interest in Microscopy Images

IEEE journal of biomedical and health informatics, 2022-08, Vol.26 (8), p.4079-4089

2022

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Pseudomonas aeruginosa Disrupts Caenorhabditis elegans Iron Homeostasis, Causing a Hypoxic Response and Death

Cell host & microbe, 2013-04, Vol.13 (4), p.406-416

2013

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High-throughput hyperdimensional vertebrate phenotyping

Nature communications, 2013, Vol.4 (1), p.1467-1467, Article 1467

2013

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Impact of Q-Griffithsin anti-HIV microbicide gel in non-human primates: In situ analyses of epithelial and immune cell markers in rectal mucosa

Scientific reports, 2019-12, Vol.9 (1), p.18120, Article 18120

2019

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Automated detection of vascular remodeling in tumor‐draining lymph nodes by the deep‐learning tool HEV‐finder

The Journal of pathology, 2022-09, Vol.258 (1), p.4-11

2022

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Graph-based image decoding for multiplexed in situ RNA detection

2020 25th International Conference on Pattern Recognition (ICPR), 2021, p.3783-3790

2021

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Blind Color Decomposition of Histological Images

IEEE transactions on medical imaging, 2013-06, Vol.32 (6), p.983-994

2013

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Spage2vec: Unsupervised representation of localized spatial gene expression signatures

Automated Training of Deep Convolutional Neural Networks for Cell Segmentation

In situ sequencing for RNA analysis in preserved tissue and cells

Introducing Hann windows for reducing edge-effects in patch-based image segmentation

TissUUmaps: interactive visualization of large-scale spatial gene expression and tissue morphology data

The quest for multiplexed spatially resolved transcriptional profiling

Deep Learning in Image Cytometry: A Review

De novo spatiotemporal modelling of cell-type signatures in the developmental human heart using graph convolutional neural networks

Label-free deep learning-based species classification of bacteria imaged by phase-contrast microscopy

Points2Regions: Fast, interactive clustering of imaging-based spatial transcriptomics data

Artificial intelligence for diagnosis and grading of prostate cancer in biopsies: a population-based, diagnostic study

PACMan: A software package for automated single‐cell chlorophyll fluorometry

TEM image restoration from fast image streams

Genes in human obesity loci are causal obesity genes in C. elegans

Regular Use of Depot Medroxyprogesterone Acetate Causes Thinning of the Superficial Lining and Apical Distribution of Human Immunodeficiency Virus Target Cells in the Human Ectocervix

Automated identification of the mouse brain's spatial compartments from in situ sequencing data

Bridging Histology and Bioinformatics-Computational Analysis of Spatially Resolved Transcriptomics

Fully automated cellular-resolution vertebrate screening platform with parallel animal processing

SimSearch: A Human-in-The-Loop Learning Framework for Fast Detection of Regions of Interest in Microscopy Images

Pseudomonas aeruginosa Disrupts Caenorhabditis elegans Iron Homeostasis, Causing a Hypoxic Response and Death

High-throughput hyperdimensional vertebrate phenotyping

Impact of Q-Griffithsin anti-HIV microbicide gel in non-human primates: In situ analyses of epithelial and immune cell markers in rectal mucosa

Automated detection of vascular remodeling in tumor‐draining lymph nodes by the deep‐learning tool HEV‐finder

Graph-based image decoding for multiplexed in situ RNA detection

Blind Color Decomposition of Histological Images

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