153 Works

The mesoSPIM initiative – open-source light-sheet microscopes for imaging cleared tissue

Fabian F. Voigt
Comparison of whole-mouse brain data acquired from a CLARITY-cleared VIP-tdTomato mouse with and without ASLM mode engaged

Identification of long noncoding RNAs in regulation of cell division.

Lovorka Stojic
Long noncoding RNAs (lncRNAs) regulate many biological processes and have been implicated in development and disease pathogenesis. The exact function for the large majority of lncRNAs is still unknown. To address whether lncRNAs could play a role in cell division, we combined a microscopy-based high-content RNAi screen with dedicated image analysis workflows to identify lncRNAs that regulate mitotic progression, chromosome segregation and cytokinesis. By targeting over 2000 lncRNAs in HeLa cells, we discovered an assortment...

The mesoSPIM initiative – open-source light-sheet microscopes for imaging cleared tissue

Fabian F. Voigt
Imaging a chicken embryo with the mesoSPIM

An Image-Based Data-Driven Analysis of Cellular Architecture in a Developing Tissue

Jonas Hartmann
3D confocal imaging of fixed samples of the zebrafish posterior lateral line primordium labeled with the membrane marker cldnB:lyn-EGFP and stained for pea3 mRNA using single molecule Fluorescence In-Situ Hybridization (smFISH).

HDBR Atlas: Gene Expression in Early Human Development

Janet Kerwin, Yiya Yang, Paloma Merchan, Subrot Sarma, Jessica Thompson, Xunxian Wang, Juan Sandoval, Luis Puelles, Richard Baldock & Susan Lindsay
Gene expression studies in early human development from 3 to 17 post conceptional weeks (PCW).

An Image-Based Data-Driven Analysis of Cellular Architecture in a Developing Tissue

Jonas Hartmann
3D confocal live imaging of the zebrafish posterior lateral line primordium labeled with the membrane marker cldnB:lyn-EGFP for segmentation and optionally with one of several additional labels.

Molecular determinants of large cargo transport into the nucleus

Joana Caria
Nucleocytoplasmic transport is tightly regulated by the nuclear pore complex (NPC). Even very large cargoes such as many pathogens, mRNAs and pre-ribosomal subunits can pass the NPC intact. Compared to small import complexes, for such large cargoes >15 nm there is very little quantitative understanding of the mechanism for efficient transport, the role of multivalent binding to nuclear transport receptors via nuclear localisation sequences (NLSs) and effects of size differences. Here, we assayed nuclear import...

High-content image-based drug screen identifies a clinical compound against cell transmission of adenovirus

Fanny Georgi
Screen Description Primary image-based screen of 1,278 mostly FDA-approved, off-patent small molecules, collected in the Prestwick Chemical Library for inhibitors of Human adenovirus infection

High-content image-based drug screen identifies a clinical compound against cell transmission of adenovirus

Fanny Georgi
Screen Description Human adenovirus infected Z' plates in biological duplicates consisting of 192 technical replicates of the solvent control DMSO and positive control DFT to confirm assay quality

The Ndc80 complex targets Bod1 to human mitotic kinetochores

Jason Swedlow & Katharina Schleicher

Ex vivo live cell tracking in kidney organoids using light sheet fluorescence microscopy

Marie Held
We have adapted the mouse kidney rudiment assay to generate renal organoids. 24 hours after pelleting 100,000 mouse kidney cells, organoids had formed in the PDMS dishes. For the PNA vital stain test we used kidney cells from wildtype mice and for the tracking time series we used cells from the Wt1tm1Nhsn strain, expressing GFP together with the transcription factor Wt1. One organoid was embedded in a hydrogel matrix (1.5% Agarose + 3% gelatine). In...

Subpopulations of sensorless bacteria drive fitness in fluctuating environments

Thomas Julou
We use quantitative time-lapse microscopy combined with microfluidics to analyse the induction dynamics of the lac operon in single bacteria cells.

A semi-automated intestinal organoid screening method demonstrates epigenetic control of epithelial maturation

Jenny Ostrop
The intestinal epithelium maintains an important barrier throughout life. It consists of several epithelial cell lineages that are derived from LGR5+ intestinal stem cells. Although epigenetic regulation of embryonic stem cell differentiation is well established, its role in adult stem cell systems such as the intestinal epithelium is still undefined. Yet, targeting of epigenetic regulatory enzymes may be relevant for new therapeutics, for example in cancer treatment. Here, we combine a newly established organoid toolbox...

Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability.

Brenda Andrews
Our ability to understand the genotype-to-phenotype relationship is hindered by the lack of detailed understanding of phenotypes at a single-cell level. To systematically assess cell-to-cell phenotypic variability, we combined automated yeast genetics, high-content screening and neural network-based image analysis of single cells, focussing on genes that influence the architecture of four subcellular compartments of the endocytic pathway as a model system. Our unbiased assessment of the morphology of these compartments — endocytic patch, actin patch,...

Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability.

Brenda Andrews
Our ability to understand the genotype-to-phenotype relationship is hindered by the lack of detailed understanding of phenotypes at a single-cell level. To systematically assess cell-to-cell phenotypic variability, we combined automated yeast genetics, high-content screening and neural network-based image analysis of single cells, focussing on genes that influence the architecture of four subcellular compartments of the endocytic pathway as a model system. Our unbiased assessment of the morphology of these compartments — endocytic patch, actin patch,...

A Deep-learning classifier identifies patients with clinical heart failure using whole-slide images of H&E tissue

Nirschl, Janowczyk, Peyster, Frank, Margulies, Feldman & Madabhushi
Cardiac histopathology from human patients with clinical heart failure or cadaveric donor hearts from patients without clinical heart failure. Human tissue research: Human heart tissue was procured from two separate groups of subjects: heart transplant or LVAD recipients with severe heart failure (Fal), and brain dead, organ donors with no history of heart failure (non-failing, NF). Tissue from patients with ischemic cardiomyopathy sampled infarct-free regions. No organs or tissue were procured from prisoners. Prospective informed...

SARS-COV-2 drug repurposing - Caco2 cell line

Bernhard Ellinger
To identify possible candidates for progression towards clinical studies against SARS-CoV-2, we screened a well-defined collection of 5632 compounds including 3488 compounds which have undergone clinical investigations (marketed drugs, phases 1 -3, and withdrawn) across 600 indications. Compounds were screened for their inhibition of viral induced cytotoxicity using the human epithelial colorectal adenocarcinoma cell line Caco-2 and a SARS-CoV-2 isolate. The primary screen of 5632 compounds gave 271 hits. A total of 64 compounds with...

Imaging Mass Cytometry of human tonsil sections

Segura
We analysed the in situ localisation of immune cell types in human tonsils using imaging mass cytometry.

Distinct Roles of Tumor Associated Mutations in Collective Cell Migration

Rachel Lee & Stuart Martin
Recent evidence suggests that groups of cells are more likely to form clinically dangerous metastatic tumors, emphasizing the importance of understanding mechanisms underlying collective behavior. The emergent collective behavior of migrating cell sheets in vitro has been shown to be disrupted in tumorigenic cells but the connection between this behavior and in vivo tumorigenicity remains unclear. We use particle image velocimetry to measure a multidimensional migration phenotype for genetically defined human breast epithelial cell lines...

In situ genome sequencing resolves DNA sequence and structure in intact biological samples

Edward S. Boyden, Jason Buenrostro & Fei Chen
Understanding genome organization requires integration of DNA sequence and 3D spatial context, however, existing genome-wide methods lack either base-pair sequence resolution or direct spatial localization. Here, we describe in situ genome sequencing (IGS), a method for simultaneously sequencing and imaging genomes within intact biological samples. We applied IGS to human fibroblasts and early mouse embryos, spatially localizing thousands of genomic loci in individual nuclei. Using these data, we characterized parent-specific changes in genome structure across...

In situ genome sequencing resolves DNA sequence and structure in intact biological samples

Edward S. Boyden, Jason Buenrostro & Fei Chen
Understanding genome organization requires integration of DNA sequence and 3D spatial context, however, existing genome-wide methods lack either base-pair sequence resolution or direct spatial localization. Here, we describe in situ genome sequencing (IGS), a method for simultaneously sequencing and imaging genomes within intact biological samples. We applied IGS to human fibroblasts and early mouse embryos, spatially localizing thousands of genomic loci in individual nuclei. Using these data, we characterized parent-specific changes in genome structure across...

Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH

Magda Bienko
We describe a dataset obtained by applying our recently developed iFISH pipeline to simultaneously visualize 16 small (size range: 62–73 kilobases, kb) evenly spaced DNA loci on chromosome 2 in human cells, in a single round of hybridization. We show how, using combinatorial color coding, multiple loci can be precisely 3D localized in single cells, and how inter-loci distances scale inversely with chromosome contact frequencies determined by Hi-C, as expected. We provide raw images and...

Quantification of within patient Staphylococcus aureus phenotypic heterogeneity as a proxy for presence of persisters across clinical presentations

Julian Baer
Staphylococcus aureus was isolated from patients suffering cardiovascular, prosthetic joint or other infections and plated on Columbia sheep blood agar. Macroscopic time-lapse imaging was performed to quantify colony appearance-time and growth-rate. As a baseline reference, the same time-lapse imaging protocol was used after subculturing clinical isolates in tryptic soy broth until bacteria reached exponential growth phase.

Quantification of within patient Staphylococcus aureus phenotypic heterogeneity as a proxy for presence of persisters across clinical presentations

Julian Baer
Staphylococcus aureus was isolated from patients suffering cardiovascular, prosthetic joint or other infections and plated on Columbia sheep blood agar. Macroscopic time-lapse imaging was performed to quantify colony appearance-time and growth-rate. As a baseline reference, the same time-lapse imaging protocol was used after subculturing clinical isolates in tryptic soy broth until bacteria reached exponential growth phase.

Registration Year

  • 2023
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Resource Types

  • Image
    153

Affiliations

  • University of Zurich
    7
  • University of Toronto
    7
  • Paul Sabatier University
    5
  • RIKEN
    3
  • National Taiwan University Hospital
    3
  • University of Massachusetts Medical School
    3
  • University of Maryland, Baltimore
    3
  • National Taiwan University
    3
  • Sunnybrook Hospital
    2
  • German Center for Integrative Biodiversity Research
    2