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Showing 1–30 of 30 results
Advanced filters: Author: Beth A. Cimini Clear advanced filters

  • This Resource presents the genetic subset of the 136,000 chemical and genetic perturbations tested by the Joint Undertaking for Morphological Profiling (JUMP) Cell Painting Consortium and associated analysis of phenotypic profiles.

    • Srinivas Niranj Chandrasekaran
    • Eric Alix
    • Anne E. Carpenter
    Research
    Nature Methods
    Volume: 22, P: 1742-1752

  • We provide an updated protocol for image-based profiling with Cell Painting. A detailed procedure, with standardized conditions for the assay, is presented, along with a comprehensive description of parameters to be considered when optimizing the assay.

    • Beth A. Cimini
    • Srinivas Niranj Chandrasekaran
    • Anne E. Carpenter
    Protocols
    Nature Protocols
    Volume: 18, P: 1981-2013

  • Pycytominer is a user-friendly, open-source Python package that carries out key bioinformatics steps in image-based profiling.

    • Erik Serrano
    • Srinivas Niranj Chandrasekaran
    • Gregory P. Way
    Research
    Nature Methods
    Volume: 22, P: 677-680

  • The CPJUMP1 Resource comprises Cell Painting images and profiles of 75 million cells treated with hundreds of chemical and genetic perturbations. The dataset enables exploration of their relationships and lays the foundation for the development of advanced methods to match perturbations.

    • Srinivas Niranj Chandrasekaran
    • Beth A. Cimini
    • Anne E. Carpenter
    ResearchOpen Access
    Nature Methods
    Volume: 21, P: 1114-1121

  • Assessing cell phenotypes in image-based assays requires solid computational methods for transforming images into quantitative data. Here, the authors present a strategy for learning representations of treatment effects from high-throughput imaging, following a causal interpretation.

    • Nikita Moshkov
    • Michael Bornholdt
    • Juan C. Caicedo
    ResearchOpen Access
    Nature Communications
    Volume: 15, P: 1-17

  • An optical pooled cell profiling platform (PERISCOPE) based on Cell Painting and optical sequencing of molecular barcodes was used to develop the first unbiased genome-wide morphology-based perturbation atlas in human cells.

    • Meraj Ramezani
    • Erin Weisbart
    • James T. Neal
    ResearchOpen Access
    Nature Methods
    Volume: 22, P: 621-633

  • Characterizing how genetic variation impacts cell morphology can provide an important links between disease association and cellular function. Here the authors identified the morphological impacts of genomic variants by generating high-throughput morphological profiling and whole genome sequencing data on iPSCs from 297 donors.

    • Matthew Tegtmeyer
    • Jatin Arora
    • Soumya Raychaudhuri
    ResearchOpen Access
    Nature Communications
    Volume: 15, P: 1-12

  • The molecular circuitry that drives dendrite formation during osteocytogenesis remains poorly understood. Here the authors show that deletion of Sp7, a gene linked to rare and common skeletal disease, in mature osteoblasts and osteocytes causes severe defects in osteocyte dendrites.

    • Jialiang S. Wang
    • Tushar Kamath
    • Marc N. Wein
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-20

  • The language used by microscopists who wish to find and measure objects in an image often differs in critical ways from that used by computer scientists who create tools to help them do this, making communication hard across disciplines. This work proposes a set of standardized questions that can guide analyses and shows how it can improve the future of bioimage analysis as a whole by making image analysis workflows and tools more FAIR (findable, accessible, interoperable and reusable).

    • Beth A. Cimini
    • Kevin W. Eliceiri
    Comments & Opinion
    Nature Methods
    Volume: 20, P: 976-978

  • Glunk et al. explore target genes and cellular mechanisms related to a metabolic obesity with normal-weight phenotype, and identify a non-coding variant that affects actin remodelling in subcutaneous adipocytes, which in turn affects the capacity of these cells to accumulate lipids.

    • Viktoria Glunk
    • Samantha Laber
    • Melina Claussnitzer
    Research
    Nature Metabolism
    Volume: 5, P: 861-879

  • The extent, origins and consequences of genetic variation within human cell lines are studied, providing a framework for researchers to measure such variation in efforts to support maximally reproducible cancer research.

    • Uri Ben-David
    • Benjamin Siranosian
    • Todd R. Golub
    Research
    Nature
    Volume: 560, P: 325-330

  • We dream of a future where light microscopes have new capabilities: language-guided image acquisition, automatic image analysis based on extensive prior training from biologist experts, and language-guided image analysis for custom analyses. Most capabilities have reached the proof-of-principle stage, but implementation would be accelerated by efforts to gather appropriate training sets and make user-friendly interfaces.

    • Anne E. Carpenter
    • Beth A. Cimini
    • Kevin W. Eliceiri
    Comments & Opinion
    Nature Methods
    Volume: 20, P: 962-964

  • Cell segmentation is crucial in many image analysis pipelines. This analysis compares many tools on a multimodal cell segmentation benchmark. A Transformer-based model performed best in terms of performance and general applicability.

    • Jun Ma
    • Ronald Xie
    • Bo Wang
    Research
    Nature Methods
    Volume: 21, P: 1103-1113

  • Metrics Reloaded is a comprehensive framework for guiding researchers in the problem-aware selection of metrics for common tasks in biomedical image analysis.

    • Lena Maier-Hein
    • Annika Reinke
    • Paul F. Jäger
    Reviews
    Nature Methods
    Volume: 21, P: 195-212

  • The 2018 Data Science Bowl challenged competitors to develop an accurate tool for segmenting stained nuclei from diverse light microscopy images. The winners deployed innovative deep-learning strategies to realize configuration-free segmentation.

    • Juan C. Caicedo
    • Allen Goodman
    • Anne E. Carpenter
    ResearchOpen Access
    Nature Methods
    Volume: 16, P: 1247-1253

  • This Perspective presents a reliable and comprehensive source of information on pitfalls related to validation metrics in image analysis, with an emphasis on biomedical imaging.

    • Annika Reinke
    • Minu D. Tizabi
    • Lena Maier-Hein
    Reviews
    Nature Methods
    Volume: 21, P: 182-194

  • The Impact of Genomic Variation on Function Consortium is combining single-cell mapping, genomic perturbations and predictive modelling to investigate relationships between human genomic variation, genome function and phenotypes and will provide an open resource to the community.

    • Jesse M. Engreitz
    • Heather A. Lawson
    • Ella K. Samer
    Reviews
    Nature
    Volume: 633, P: 47-57

  • Tomov et al. utilize DNA-PRISM to allow for multiplexed imaging of cultured cells using antibodies modified with oligonucleotide probes. The differentiation of iPSCs to cortical and motor neurons is characterized in model cultures, relevant for use in disease research and drug screening.

    • Martin L. Tomov
    • Alison O’Neil
    • Mark Bathe
    ResearchOpen Access
    Communications Biology
    Volume: 4, P: 1-9