4,309 research outputs found
How to understand the cell by breaking it: network analysis of gene perturbation screens
Modern high-throughput gene perturbation screens are key technologies at the
forefront of genetic research. Combined with rich phenotypic descriptors they
enable researchers to observe detailed cellular reactions to experimental
perturbations on a genome-wide scale. This review surveys the current
state-of-the-art in analyzing perturbation screens from a network point of
view. We describe approaches to make the step from the parts list to the wiring
diagram by using phenotypes for network inference and integrating them with
complementary data sources. The first part of the review describes methods to
analyze one- or low-dimensional phenotypes like viability or reporter activity;
the second part concentrates on high-dimensional phenotypes showing global
changes in cell morphology, transcriptome or proteome.Comment: Review based on ISMB 2009 tutorial; after two rounds of revisio
Morphological Profiling for Drug Discovery in the Era of Deep Learning
Morphological profiling is a valuable tool in phenotypic drug discovery. The
advent of high-throughput automated imaging has enabled the capturing of a wide
range of morphological features of cells or organisms in response to
perturbations at the single-cell resolution. Concurrently, significant advances
in machine learning and deep learning, especially in computer vision, have led
to substantial improvements in analyzing large-scale high-content images at
high-throughput. These efforts have facilitated understanding of compound
mechanism-of-action (MOA), drug repurposing, characterization of cell
morphodynamics under perturbation, and ultimately contributing to the
development of novel therapeutics. In this review, we provide a comprehensive
overview of the recent advances in the field of morphological profiling. We
summarize the image profiling analysis workflow, survey a broad spectrum of
analysis strategies encompassing feature engineering- and deep learning-based
approaches, and introduce publicly available benchmark datasets. We place a
particular emphasis on the application of deep learning in this pipeline,
covering cell segmentation, image representation learning, and multimodal
learning. Additionally, we illuminate the application of morphological
profiling in phenotypic drug discovery and highlight potential challenges and
opportunities in this field.Comment: 44 pages, 5 figure, 5 table
Clustering phenotype populations by genome-wide RNAi and multiparametric imaging
How to predict gene function from phenotypic cues is a longstanding question in biology.Using quantitative multiparametric imaging, RNAi-mediated cell phenotypes were measured on a genome-wide scale.On the basis of phenotypic ‘neighbourhoods', we identified previously uncharacterized human genes as mediators of the DNA damage response pathway and the maintenance of genomic integrity.The phenotypic map is provided as an online resource at http://www.cellmorph.org for discovering further functional relationships for a broad spectrum of biological modul
From observing to predicting single-cell structure and function with high-throughput/high-content microscopy
Abstract In the past 15 years, cell-based microscopy has evolved its focus from observing cell function to aiming to predict it. In particular—powered by breakthroughs in computer vision, large-scale image analysis and machine learning—high-throughput and high-content microscopy imaging have enabled to uniquely harness single-cell information to systematically discover and annotate genes and regulatory pathways, uncover systems-level interactions and causal links between cellular processes, and begin to clarify and predict causal cellular behaviour and decision making. Here we review these developments, discuss emerging trends in the field, and describe how single-cell ‘omics and single-cell microscopy are imminently in an intersecting trajectory. The marriage of these two fields will make possible an unprecedented understanding of cell and tissue behaviour and function
Masked Autoencoders are Scalable Learners of Cellular Morphology
Inferring biological relationships from cellular phenotypes in high-content
microscopy screens provides significant opportunity and challenge in biological
research. Prior results have shown that deep vision models can capture
biological signal better than hand-crafted features. This work explores how
self-supervised deep learning approaches scale when training larger models on
larger microscopy datasets. Our results show that both CNN- and ViT-based
masked autoencoders significantly outperform weakly supervised baselines. At
the high-end of our scale, a ViT-L/8 trained on over 3.5-billion unique crops
sampled from 93-million microscopy images achieves relative improvements as
high as 28% over our best weakly supervised baseline at inferring known
biological relationships curated from public databases. Relevant code and
select models released with this work can be found at:
https://github.com/recursionpharma/maes_microscopy.Comment: Spotlight at NeurIPS 2023 Generative AI and Biology (GenBio) Worksho
Data-analysis strategies for image-based cell profiling
Image-based cell profiling is a high-throughput strategy for the quantification of phenotypic differences among a variety of cell populations. It paves the way to studying biological systems on a large scale by using chemical and genetic perturbations. The general workflow for this technology involves image acquisition with high-throughput microscopy systems and subsequent image processing and analysis. Here, we introduce the steps required to create high-quality image-based (i.e., morphological) profiles from a collection of microscopy images. We recommend techniques that have proven useful in each stage of the data analysis process, on the basis of the experience of 20 laboratories worldwide that are refining their image-based cell-profiling methodologies in pursuit of biological discovery. The recommended techniques cover alternatives that may suit various biological goals, experimental designs, and laboratories' preferences.Peer reviewe
Evolution and Impact of High Content Imaging
Abstract/outline: The field of high content imaging has steadily evolved and expanded substantially across many industry and academic research institutions since it was first described in the early 1990′s. High content imaging refers to the automated acquisition and analysis of microscopic images from a variety of biological sample types. Integration of high content imaging microscopes with multiwell plate handling robotics enables high content imaging to be performed at scale and support medium- to high-throughput screening of pharmacological, genetic and diverse environmental perturbations upon complex biological systems ranging from 2D cell cultures to 3D tissue organoids to small model organisms. In this perspective article the authors provide a collective view on the following key discussion points relevant to the evolution of high content imaging:• Evolution and impact of high content imaging: An academic perspective• Evolution and impact of high content imaging: An industry perspective• Evolution of high content image analysis• Evolution of high content data analysis pipelines towards multiparametric and phenotypic profiling applications• The role of data integration and multiomics• The role and evolution of image data repositories and sharing standards• Future perspective of high content imaging hardware and softwar
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