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

Autor: Nathalie Aulner, Spencer L. Shorte, Sébastien Herbert, Elric Esposito, Romain Levayer, Laure Bally-Cuif, Jean-Yves Tinevez, Jerome Gros, Paolo Caldarelli, Laure Mancini, Léo Valon, Nicolas Dray
Přispěvatelé: Hub d'analyse d'images - Image Analysis Hub (Platform) (IAH), Institut Pasteur [Paris] (IP), Mort cellulaire et homéostasie des épithéliums / Cell death and epithelial homeostasis, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Neurogénétique du Poisson zébré / Zebrafish Neurogenetics, Collège Doctoral, Sorbonne Université (SU), Régulation Dynamique de la Morphogénèse - Dynamic Regulation of Morphogenesis, BioImagerie Photonique – Photonic BioImaging (UTechS PBI), This work was supported by the Labex REVIVE (Investissement d’Avenir, ANR-10-LABX-73), France BioImaging (Investissement d’Avenir, ANR-10–INSB–04) and the Région Île-de-France in the framework of DIM ELICIT. Work in the R. L. laboratory is supported by the Institut Pasteur (G5 starting package), a ERC starting grant (CoSpaDD, #758457), the 'Cercle FSER' and the CNRS (UMR 3738). L. V. is supported by a Post-doctoral grant 'Aide au 224 Retour en France' from the Fondation pour la Recherche Médicale (ARF20170938651) and a Marie Sklodowska-Curie postdoctoral fellowship (MechDeath, 789573). Work in the J. G. laboratory was supported by the European Research Council under the European Union’s Seventh Framework Program (FP7/2007-2013) / ERC Grant Agreement no. 337635. P. C. is sponsored by the Institut Pasteur and the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska Curie (665807). Work in the L. B-C. laboratory was supported by the Ligue Nationale Contre le Cancer and the European Research Council (AdG 322936). L. M. was recipient of a PhD student fellowship from the Fondation pour la Recherche Médicale., ANR-10-LABX-0073,REVIVE,Stem Cells in Regenerative Biology and Medicine(2010), European Project: 758457,H2020-EU.1.1. - EXCELLENT SCIENCE - European Research Council (ERC),ERC-2017-STG,CoSpaDD(2018), European Project: 789573,FP7-IDEAS-ERC - Specific programme: 'Ideas' implementing the Seventh Framework Programme of the European Community for research, technological development and demonstration activities (2007 to 2013),H2020-MSCA-IF-2017,MechDeath(2019), European Project: 337635,EC:FP7:ERC,ERC-2013-StG,LIMBCELLDYNAMICS(2014), European Project: 665807,H2020,H2020-MSCA-COFUND-2014,PASTEURDOC(2015), European Project: 322936,EC:FP7:ERC,ERC-2012-ADG_20120314,SYSTEMATICS(2013), ANR-10-LABX-73), France BioImaging (Investissement d’ Avenir, ANR-10–INSB–04) and the Région Île-de-France in the framework of DIM ELICIT. Work in the R. L. laboratory is supported by the Institut Pasteur (G5 starting package), a ERC starting grant (CoSpaDD, #758457), the 'Cercle FSER' and the CNRS (UMR 3738). L. V. is supported by a Postdoctoral grant 'Aide au 224 Retour en France' from the Fondation pour la Recherche Médicale (ARF20170938651) and a Marie Sklodowska-Curie postdoctoral fellowship (MechDeath, 789573). Work in the J. G. laboratory was supported by the European Research Council under the European Union’s Seventh Framework Program (FP7/2007-2013) / ERC Grant Agreement no. 337635. P. C. is sponsored by the Institut Pasteur and the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska Curie (665807). Work in the L. B-C. laboratory was supported by the Ligue Nationale Contre le Cancer and the European Research Council (AdG 322936). L. M. was recipient of a PhD student fellowship from the Fondation pour la Recherche Médicale., ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), Centre de Ressources et de Recherche Technologique - Center for Technological Resources and Research (C2RT), Institut Pasteur [Paris]-Institut Pasteur [Paris], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Neurogénétique du Poisson zébré - Zebrafish Neurogenetics, Collège doctoral [Sorbonne universités], Sorbonne Université, Institut Pasteur [Paris], Département de Biologie du Développement et Cellules souches - Department of Developmental and Stem Cell Biology
Jazyk: angličtina
Rok vydání: 2021
Předmět:
Zdroj: BMC Biology
BMC Biology, 2021, 19 (1), pp.136. ⟨10.1186/s12915-021-01037-w⟩
BMC Biology, 2021, ⟨10.1101/2021.01.15.426809⟩
BMC Biology, Vol 19, Iss 1, Pp 1-13 (2021)
BMC Biology, BioMed Central, 2021, ⟨10.1101/2021.01.15.426809⟩
BMC Biology, BioMed Central, 2021, 19 (1), pp.136. ⟨10.1186/s12915-021-01037-w⟩
ISSN: 1741-7007
DOI: 10.1186/s12915-021-01037-w⟩
Popis: BackgroundQuantitative imaging of epithelial tissues prompts for bioimage analysis tools that are widely applicable and accurate. In the case of imaging 3D tissues, a common pre-processing step consists in projecting the acquired 3D volume on a 2D plane mapping the tissue surface. Indeed, 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 user-friendly and 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 un-wanted 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.
Databáze: OpenAIRE
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