Fabian Theis
Principal investigator
Single-cell genomics · Perturbation responses · Bulk omics and genetics
Topics · Data · Images and health records
Imaging
Work whose data are images, such as microscopy, histology, imaging flow cytometry, retinal scans or brain imaging, including their analysis, for example segmentation. Not for figures or plots of other data.
In Data › Images and health records92 works1 person8 tools
People1
AlumniIlan Gold
Publications92
Pan-cancer virtual spatial transcriptomics from routine histology with Phoenix
Beyond alignment: synergistic integration is required for multimodal cell foundation models
From modality-specific to compositional foundation models for cell biology
DISCO-seq: 3D single-cell transcriptomics of intact biological systems
Exploration of RNA outside segmented cells in spatial transcriptomics reveals extrasomatic RNA organization
Advancing spatial biology analysis across programming languages
scPortrait integrates single-cell images into multimodal modeling
Im-seq: Multimodal droplet barcoding enables high-throughput linking of single-cell imaging and gene expression
Predicting cell morphological responses to perturbations using generative modeling
Vitessce: integrative visualization of multimodal and spatially resolved single-cell data
Mode of actions of nanomaterial-induced respiratory toxicity
An open-source framework for end-to-end analysis of electronic health record data
Polyploidisation pleiotropically buffers ageing in hepatocytes
Evaluation of OCT biomarker changes in treatment-naive neovascular AMD using a deep semantic segmentation algorithm
SpatialData: an open and universal data framework for spatial omics
Deep Learning-Based Retinal Layer Segmentation in Optical Coherence Tomography Scans of Patients with Inherited Retinal Diseases
Exploratory electronic health record analysis with ehrapy
Explainable machine learning for profiling the immunological synapse and functional characterization of therapeutic antibodies
A spatially resolved extracellular matrix proteome atlas of the distal human lung
Distinct molecular profiles of skull bone marrow in health and neurological disorders
OME-Zarr: a cloud-optimized bioimaging file format with international community support
Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps
Deciphering subcellular organization with multiplexed imaging and deep learning
Spatial proteomics in three-dimensional intact specimens
Interpretable surface-based detection of focal cortical dysplasias: a Multi-centre Epilepsy Lesion Detection study
Squidpy: a scalable framework for spatial omics analysis
Noise Transfer for Unsupervised Domain Adaptation of Retinal OCT Images
Multi-omics and 3D-imaging reveal bone heterogeneity and unique calvaria cells in neuroinflammation
SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis
CD81 marks immature and dedifferentiated pancreatic β-cells
Swarm Learning for decentralized and confidential clinical machine learning
Posterior subcapsular cataracts are a late effect after acute exposure to 0.5 Gy ionizing radiation in mice
Squidpy: a scalable framework for spatial single cell analysis
A sparse deep learning approach for automatic segmentation of human vasculature in multispectral optoacoustic tomography
Conditional out-of-distribution generation for unpaired data using transfer VAE
Self-supervised retinal thickness prediction enables deep learning from unlabelled data to boost classification of diabetic retinopathy
Predicting single-cell gene expression profiles of imaging flow cytometry data with machine learning
LifeTime and improving European healthcare through cell-based interceptive medicine
In vivo identification of apoptotic and extracellular vesicle‐bound live cells using image‐based deep learning
Pheno-seq – linking visual features and gene expression in 3D cell culture systems
Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images
Altered relaxation times in MRI indicate bronchopulmonary dysplasia
Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data
Is the humoral immunity dispensable for the pathogenesis of psoriasis?
Inductive and Selective Effects of GSK3 and MEK Inhibition on Nanog Heterogeneity in Embryonic Stem Cells
Lifetime study in mice after acute low-dose ionizing radiation: a multifactorial study with special focus on cataract risk
Reconstructing cell cycle and disease progression using deep learning
A BaSiC tool for background and shading correction of optical microscopy images
fastER: a user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy
Prospective identification of hematopoietic lineage choice by deep learning
Calcium-regulatory proteins as modulators of chemotherapy in human neuroblastoma
Label Free Identification of Peripheral Blood Eosinophils Using High-Throughput Imaging Flow Cytometry
AURKA, DLGAP5, TPX2, KIF11 and CKAP5: Five specific mitosis-associated genes correlate with poor prognosis for non-small cell lung cancer patients
Analysis of Cell Lineage Trees by Exact Bayesian Inference Identifies Negative Autoregulation of Nanog in Mouse Embryonic Stem Cells
A novel molecular disease classifier for psoriasis and eczema
LSC Abstract – Early biomarkers indicating the development of neonatal chronic lung disease defined by clinical and imaging parameters
Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios
MEMO: multi-experiment mixture model analysis of censored data
Label-free cell cycle analysis for high-throughput imaging flow cytometry
Mitosis Detection in Intestinal Crypt Images with Hough Forest and Conditional Random Fields
Quantitative comparison of competing PDE models for Pomlp dynamics in fission yeast * *The authors acknowledge financial support from the Postdoctoral Fellowship Program (PFP) of the Helmholtz Zentrum Munchen.
Inference of spatiotemporal effects on cellular state transitions from time-lapse microscopy
Live imaging of adult neural stem cell behavior in the intact and injured zebrafish brain
Anatomic-landmark detection using graphical context modelling
Cytokine-Regulated GADD45G Induces Differentiation and Lineage Selection in Hematopoietic Stem Cells
An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy
Wound-healing growth factor, basic FGF, induces Erk1/2-dependent mechanical hyperalgesia
Modeling of 2D diffusion processes based on microscopy data: parameter estimation and practical identifiability analysis
Live imaging of astrocyte responses to acute injury reveals selective juxtavascular proliferation
Multi‐scale modeling of GMP differentiation based on single‐cell genealogies
The Sox17‐mCherry fusion mouse line allows visualization of endoderm and vascular endothelial development
Colored Subspace Analysis: Dimension Reduction Based on a Signal's Autocorrelation Structure
Robust Second-Order Source Separation Identifies Experimental Responses in Biomedical Imaging
ICA, kernel methods and nonnegativity: New paradigms for dynamical component analysis of fMRI data
Blind Source Separation Techniques for the Decomposition of Multiply Labeled Fluorescence Images
Blind Source Separation Techniques For The Decomposition Of Multiply Labeled Fluorescence Images
Blind Decomposition of Spectral Imaging Microscopy: A Study on Artificial and Real Test Data
Effective Emission Tomography Image Reconstruction Algorithms for SPECT Data
A Toolbox for Model-Free Analysis of fMRI Data
A Fast Predictive Lossless Coder for fMRI Data Sets
Optimization Algorithms for Sparse Representations and Applications
Functional MRI Analysis by a Novel Spatiotemporal ICA Algorithm
A Fast and Efficient Method for Compressing fMRI Data Sets
Tree-dependent and topographic independent component analysis for fMRI analysis
3D Spatial Analysis of fMRI Data on a Word Perception Task
Spatial ICA of fMRI data in time windows
Blind source separation and sparse component analysis of overcomplete mixtures
Clustering of dependent components: a new paradigm for fMRI signal detection
Denoising using local ICA and kernel-PCA
3D spatial analysis of fMRI data: a comparison of ICA and GLM analysis on a word perception task
Blind Sensor Characteristics Estimation in a Multi-Sensor Network Applied to fMRI Analysis
Local features in biomedical image clusters extracted with independent component analysis
Software8
Squidpy
Spatial Single Cell Analysis in Python
612v1.8.49 d agoPython
spatialdata-plot
Static plotting for spatialdata
89v0.4.329 d agoPython
IMPA
29IMPA-v1.0.024 mo agoJupyter Notebook
embpy
23v0.1.14 mo agoPython
campa
Conditional Autoencoders for Multiplexed Pixel Analysis
19v1.1.04 y agoJupyter Notebook
mantispy
Analysis framework for morphological profiling data
15v0.1.0a36 d agoPython
sprotmetrics
Quality metrics for imaging-based spatial proteomics: segmentation, signal-to-background, normalization, marker distribution and technical-covariate diagnostics.
2v0.1.019 d agoPython
ifcseq
IFC-Seq: predicting single-cell gene expression for Imaging Flow Cytometry data
1Jupyter Notebook