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Herbert S, Valon L, Mancini L, et al. LocalZProjector and DeProj: a toolbox for local 2D projection and accurate morphometrics of large 3D microscopy images. BMC Biol. 2021;19(1):136doi: 10.1186/s12915-021-01037-w.
Herbert, S., Valon, L., Mancini, L., Dray, N., Caldarelli, P., Gros, J., Esposito, E., Shorte, S. L., Bally-Cuif, L., Aulner, N., Levayer, R., & Tinevez, J. Y. (2021). LocalZProjector and DeProj: a toolbox for local 2D projection and accurate morphometrics of large 3D microscopy images. BMC biology, 19(1), 136. https://doi.org/10.1186/s12915-021-01037-w
Herbert, Sébastien, et al. "LocalZProjector and DeProj: a toolbox for local 2D projection and accurate morphometrics of large 3D microscopy images." BMC biology vol. 19,1 (2021): 136. doi: https://doi.org/10.1186/s12915-021-01037-w
Herbert S, Valon L, Mancini L, Dray N, Caldarelli P, Gros J, Esposito E, Shorte SL, Bally-Cuif L, Aulner N, Levayer R, Tinevez JY. LocalZProjector and DeProj: a toolbox for local 2D projection and accurate morphometrics of large 3D microscopy images. BMC Biol. 2021 Jul 02;19(1):136. doi: 10.1186/s12915-021-01037-w. PMID: 34215263; PMCID: PMC8254216.
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BMC Biol. 2021 Jul 02;19(1):136. doi: 10.1186/s12915-021-01037-w.

LocalZProjector and DeProj: a toolbox for local 2D projection and accurate morphometrics of large 3D microscopy images.

BMC biology

Sébastien Herbert, Léo Valon, Laure Mancini, Nicolas Dray, Paolo Caldarelli, Jérôme Gros, Elric Esposito, Spencer L Shorte, Laure Bally-Cuif, Nathalie Aulner, Romain Levayer, Jean-Yves Tinevez

Affiliations

  1. Image Analysis Hub, C2RT / DTPS, Institut Pasteur, Paris, France.
  2. Present Address: Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland.
  3. Cell death and epithelial homeostasis unit, Developmental and Stem Cell Biology Department, UMR3738 CNRS, Institut Pasteur, Paris, France.
  4. Zebrafish Neurogenetics unit (Team supported by the Ligue Nationale Contre le Cancer), Developmental and Stem Cell Biology Department, UMR3738 CNRS, Institut Pasteur, Paris, France.
  5. Collège doctoral, Sorbonne Université, Paris, France.
  6. Dynamic Regulation of Morphogenesis, Developmental and Stem Cell Biology Department, UMR3738 CNRS, Institut Pasteur, Paris, France.
  7. UTechS PBI, C2RT / DTPS, Institut Pasteur, Paris, France.
  8. Image Analysis Hub, C2RT / DTPS, Institut Pasteur, Paris, France. [email protected].

PMID: 34215263 PMCID: PMC8254216 DOI: 10.1186/s12915-021-01037-w

Abstract

BACKGROUND: Quantitative 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.

RESULTS: Here 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.

CONCLUSIONS: We 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.

Keywords: 3D imaging; Image analysis; Morphology; Tissue imaging

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