Single Cell Fluorescence Ratio Image Analysis for Studying ESCRT Function in Receptor Trafficking

2019 ◽  
pp. 93-103
Author(s):  
Jalal M. Kazan ◽  
Gergely L. Lukacs ◽  
Pirjo M. Apaja ◽  
Arnim Pause
Keyword(s):  
Image Analysis ◽  
Single Cell ◽  
Receptor Trafficking ◽  
Fluorescence Ratio ◽  
Ratio Image

scholarly journals ME-VAE: Multi-Encoder Variational AutoEncoder for Controlling Multiple Transformational Features in Single Cell Image Analysis

2021 ◽  
Author(s):  
Luke Ternes ◽  
Mark Dane ◽  
Marilyne Labrie ◽  
Gordon Mills ◽  
Joe Gray ◽  
...  
Keyword(s):  
Image Analysis ◽  
Single Cell ◽  
Imaging Features ◽  
Phenotypic Differences ◽  
Cell Image ◽  
Intensity Measurements ◽  
Quantitative Measurements ◽  
Variational Autoencoder ◽  
Cell Image Analysis ◽  
Organizational Features

AbstractImage-based cell phenotyping relies on quantitative measurements as encoded representations of cells; however, defining suitable representations that capture complex imaging features is challenging since there are many obstacles, including segmentation and identifying subcellular compartments for feature extraction. Variational autoencoder (VAE) approaches produce encouraging results by mapping from an image to a representative descriptor, and outperform classical hand-crafted features for morphology, intensity, and texture at differentiating data. Although VAEs show promising results for capturing morphological and organizational features in tissue, single cell image analyses based on VAEs often fail to identify biologically informative features due to the intrinsic amount of uninformative variability. Herein, we propose a multi-encoder VAE (ME-VAE) in single cell image analysis using transformed images as a self-supervised signal to extract transform-invariant biologically meaningful features. We show that the proposed architecture improves analysis by making distinct populations more separable compared to traditional VAEs and intensity measurements by enhancing phenotypic differences between cells and by improving correlations to other modalities.

scholarly journals 3D magnetically controlled spatiotemporal probing and actuation of collagen networks from a single cell perspective

Lab on a Chip ◽  
2021 ◽  
Vol 21 (20) ◽  
pp. 3850-3862
Author(s):  
Daphne O. Asgeirsson ◽  
Michael G. Christiansen ◽  
Thomas Valentin ◽  
Luca Somm ◽  
Nima Mirkhani ◽  
...  
Keyword(s):  
Magnetic Field ◽  
Extracellular Matrix ◽  
Image Analysis ◽  
Matrix Models ◽  
Single Cell ◽  
Physical Modeling ◽  
Single Cells ◽  
Field Control

Rod-shaped magnetic microprobes are employed to assess and actuate extracellular matrix models in 3D from the perspective of single cells. To achieve this, our method combines magnetic field control, physical modeling, and image analysis.

scholarly journals Single-cell image analysis reveals a protective role for microglia in glioblastoma

2021 ◽  
Author(s):  
Zoe Woolf ◽  
Molly E V Swanson ◽  
Leon C Smyth ◽  
Edward W Mee ◽  
Patrick Schweder ◽  
...  
Keyword(s):  
Image Analysis ◽  
Single Cell ◽  
Patient Survival ◽  
Myeloid Cells ◽  
Protective Role ◽  
Low Grade ◽  
Tumour Mass ◽  
Tissue Sections ◽  
Cd163 Expression ◽  
Cell Image Analysis

Abstract Background Microglia and tumour associated macrophages (TAMs) constitute up to half of the total tumour mass of glioblastomas. Despite these myeloid populations being ontogenetically distinct, they have been largely conflated. Recent single-cell transcriptomic studies have identified genes that distinguish microglia from TAMs. Here we investigated whether the transcribed proteins of genes enriched in microglial or TAM populations can be used to differentiate these myeloid cells in immunohistochemically stained human glioblastoma tissue. Methods Tissue sections from resected low-grade, meningioma, and glioblastoma (grade IV) tumours and epilepsy tissues were immunofluorescently triple-labelled for Iba1 (pan-myeloid marker), CD14 or CD163 (preferential TAM-markers) and either P2RY12 or TMEM119 (microglial-specific markers). Using a single cell-based image analysis pipeline, we quantified the abundance of each marker within single myeloid cells, allowing the identification and analysis of myeloid populations. Results P2RY12 and TMEM119 successfully discriminated microglia from TAMs in glioblastoma. In contrast, CD14 and CD163 expression were not restricted to invading TAMs, and were upregulated by tumour microglia. Notably, a higher ratio of microglia-to-TAMs significantly correlated with increased patient survival. Conclusions We demonstrate the validity of previously defined microglial-specific genes P2RY12 and TMEM119 as robust discriminators of microglia and TAMs at the protein level in human tissue. Moreover, our data suggests that a higher proportion of microglia may be beneficial for patient survival in glioblastoma. Accordingly, this tissue-based method for myeloid population differentiation could serve as a useful prognostic tool.

scholarly journals An Automated, Single Cell Quantitative Imaging Microscopy Approach to Assess Micronucleus Formation, Genotoxicity and Chromosome Instability

Cells ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 344 ◽  
Author(s):  
Chloe C. Lepage ◽  
Laura L. Thompson ◽  
Bradley Larson ◽  
Kirk J. McManus
Keyword(s):  
Image Analysis ◽  
Single Cell ◽  
Large Scale ◽  
Quantitative Imaging ◽  
Chromosome Instability ◽  
Genotoxic Stress ◽  
Automated Image Analysis ◽  
Micronucleus Formation ◽  
Distinct Cell ◽  
Efficient Alternative

Micronuclei are small, extranuclear bodies that are distinct from the primary cell nucleus. Micronucleus formation is an aberrant event that suggests a history of genotoxic stress or chromosome mis-segregation events. Accordingly, assays evaluating micronucleus formation serve as useful tools within the fields of toxicology and oncology. Here, we describe a novel micronucleus formation assay that utilizes a high-throughput imaging platform and automated image analysis software for accurate detection and rapid quantification of micronuclei at the single cell level. We show that our image analysis parameters are capable of identifying dose-dependent increases in micronucleus formation within three distinct cell lines following treatment with two established genotoxic agents, etoposide or bleomycin. We further show that this assay detects micronuclei induced through silencing of the established chromosome instability gene, SMC1A. Thus, the micronucleus formation assay described here is a versatile and efficient alternative to more laborious cytological approaches, and greatly increases throughput, which will be particularly beneficial for large-scale chemical or genetic screens.

scholarly journals Single-Cell FRET Imaging of Transferrin Receptor Trafficking Dynamics by Sfp-Catalyzed, Site-Specific Protein Labeling

2005 ◽  
Vol 12 (9) ◽  
pp. 999-1006 ◽  
Author(s):  
Jun Yin ◽  
Alison J. Lin ◽  
Peter D. Buckett ◽  
Marianne Wessling-Resnick ◽  
David E. Golan ◽  
...  
Keyword(s):  
Single Cell ◽  
Transferrin Receptor ◽  
Specific Protein ◽  
Receptor Trafficking ◽  
Protein Labeling ◽  
Site Specific
Sign in / Sign up

Export Citation Format

Share Document