ArticleBMC biology2022
Griottes: a generalist tool for network generation from segmented tissue images.
Article in BMC biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Hypoxia shapes both therapeutic response and resistance in metastatic clear cell renal cell carcinoma.Cancer cell · 2026Article
- Automated Feature Segmentation of Ultra-Widefield OCT Images.Ophthalmology science · 2026Article
- From cells to pixels: A decision tree for designing bioimage analysis pipelines.Journal of microscopy · 2025Article
- CellMet: Extracting 3D shape and topology metrics from confluent cells within tissues.PLoS computational biology · 2025Article
- CD103+CD56+ ILCs Are Associated with an Altered CD8+ T-cell Profile within the Tumor Microenvironment.Cancer immunology research · 2025Article
- Polarity-JaM: an image analysis toolbox for cell polarity, junction and morphology quantification.Nature communications · 2025Article
- Spatiotemporal dynamics of fetal liver hematopoietic niches.The Journal of experimental medicine · 2025Article
- Homebuilt Imaging-Based Spatial Transcriptomics: Tertiary Lymphoid Structures as a Case Example.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Tissues as networks of cells: towards generative rules of complex organ development.Journal of the Royal Society, Interface · 2023Review
- The promise and challenge of spatial omics in dissecting tumour microenvironment and the role of AI.Frontiers in oncology · 2023Review
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMicroscopy techniques and image segmentation algorithms have improved dramatically this decade, leading to an ever increasing amount of biological images and a greater reliance on imaging to investigate biological questions. This has created a need for methods to extract the relevant information on the behaviors of cells and their interactions, while reducing the amount of computing power required to organize this information.
resultsThis task can be performed by using a network representation in which the cells and their properties are encoded in the nodes, while the neighborhood interactions are encoded by the links. Here, we introduce Griottes, an open-source tool to build the "network twin" of 2D and 3D tissues from segmented microscopy images. We show how the library can provide a wide range of biologically relevant metrics on individual cells and their neighborhoods, with the objective of providing multi-scale biological insights. The library's capacities are demonstrated on different image and data types.
conclusionsThis library is provided as an open-source tool that can be integrated into common image analysis workflows to increase their capacities.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.