ArticleBMC biology2021
LocalZProjector and DeProj: a toolbox for local 2D projection and accurate morphometrics of large 3D microscopy images.
Article in BMC biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Short-term memory of past caspase activity biases cell elimination in vivo.Nature communications · 2026Article
- Successful oocyte transport through the oviduct does not depend on the longitudinal alignment of oviduct epithelial folds.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Elevated temperature fatally disrupts nuclear divisions in the early Drosophila embryo.Nature communications · 2026Article
- Quantitative live imaging reveals PRICKLE1 controls junctional neural tube morphogenesis independent of Planar Cell Polarity.Nature communications · 2026Article
- FishFeats: streamlined quantification of multimodal labeling at the single-cell level in 3D tissues.Bioinformatics (Oxford, England) · 2026Article
- Dynamics of supracellular keratin bundling and nuclear uncaging in stretched epithelia.Nature physics · 2026Article
- Shaping 3D minimal model tissues with mechanical constraints to orchestrate muscle differentiation.Communications biology · 2025Article
- Epithelial tension controls intestinal cell extrusion.Science (New York, N.Y.) · 2025Article
- Blender tissue cartography: an intuitive tool for the analysis of dynamic 3D microscopy data.bioRxiv : the preprint server for biology · 2025Article
- EGFR-dependent actomyosin patterning coordinates morphogenetic movements between tissues in Drosophila melanogaster.Developmental cell · 2025Article
- Artificial Intelligence in the Non-Invasive Detection of Melanoma.Life (Basel, Switzerland) · 2024Review
- Single-cell morphometrics reveals T-box gene-dependent patterns of epithelial tension in the Second Heart field.Nature communications · 2024Article
- Patterned apoptosis has an instructive role for local growth and tissue shape regulation in a fast-growing epithelium.Current biology : CB · 2024Article
- EGFR-dependent actomyosin patterning coordinates morphogenetic movements between tissues.bioRxiv : the preprint server for biology · 2023Article
- TubULAR: tracking in toto deformations of dynamic tissues via constrained maps.Nature methods · 2023Article
- VolumePeeler: a novel FIJI plugin for geometric tissue peeling to improve visualization and quantification of 3D image stacks.BMC bioinformatics · 2023Article
- DeXtrusion: automatic recognition of epithelial cell extrusion through machine learning in vivo.Development (Cambridge, England) · 2023Article
- Mechano-chemical regulation of complex cell shape formation: Epidermal pavement cells-A case study.Quantitative plant biology · 2023Review
- DeepProjection: specific and robust projection of curved 2D tissue sheets from 3D microscopy using deep learning.Development (Cambridge, England) · 2022Article
- Eya-controlled affinity between cell lineages drives tissue self-organization during Drosophila oogenesis.Nature communications · 2022Article
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12 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundQuantitative imaging of epithelial tissues requires bioimage analysis tools that are widely applicable and accurate. In the case of imaging 3D tissues, a common preprocessing step consists of projecting the acquired 3D volume on a 2D plane mapping the tissue surface. While segmenting the tissue cells is amenable on 2D projections, it is still very difficult and cumbersome in 3D. However, for many specimen and models used in developmental and cell biology, the complex content of the image volume surrounding the epithelium in a tissue often reduces the visibility of the biological object in the projection, compromising its subsequent analysis. In addition, the projection may distort the geometry of the tissue and can lead to strong artifacts in the morphology measurement.
resultsHere we introduce a user-friendly toolbox built to robustly project epithelia on their 2D surface from 3D volumes and to produce accurate morphology measurement corrected for the projection distortion, even for very curved tissues. Our toolbox is built upon two components. LocalZProjector is a configurable Fiji plugin that generates 2D projections and height-maps from potentially large 3D stacks (larger than 40 GB per time-point) by only incorporating signal of the planes with local highest variance/mean intensity, despite a possibly complex image content. DeProj is a MATLAB tool that generates correct morphology measurements by combining the height-map output (such as the one offered by LocalZProjector) and the results of a cell segmentation on the 2D projection, hence effectively deprojecting the 2D segmentation in 3D. In this paper, we demonstrate their effectiveness over a wide range of different biological samples. We then compare its performance and accuracy against similar existing tools.
conclusionsWe find that LocalZProjector performs well even in situations where the volume to project also contains unwanted signal in other layers. We show that it can process large images without a pre-processing step. We study the impact of geometrical distortions on morphological measurements induced by the projection. We measured very large distortions which are then corrected by DeProj, providing accurate outputs.
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