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Article ; Online: A stochastic framework to model axon interactions within growing neuronal populations.

Razetti, Agustina / Medioni, Caroline / Malandain, Grégoire / Besse, Florence / Descombes, Xavier

2018 Volume 14, Issue 12, Page(s) e1006627

Abstract: The confined and crowded environment of developing brains imposes spatial constraints on neuronal cells that have evolved individual and collective strategies to optimize their growth. These include organizing neurons into populations extending their ... ...

Abstract	The confined and crowded environment of developing brains imposes spatial constraints on neuronal cells that have evolved individual and collective strategies to optimize their growth. These include organizing neurons into populations extending their axons to common target territories. How individual axons interact with each other within such populations to optimize innervation is currently unclear and difficult to analyze experimentally in vivo. Here, we developed a stochastic model of 3D axon growth that takes into account spatial environmental constraints, physical interactions between neighboring axons, and branch formation. This general, predictive and robust model, when fed with parameters estimated on real neurons from the Drosophila brain, enabled the study of the mechanistic principles underlying the growth of axonal populations. First, it provided a novel explanation for the diversity of growth and branching patterns observed in vivo within populations of genetically identical neurons. Second, it uncovered that axon branching could be a strategy optimizing the overall growth of axons competing with others in contexts of high axonal density. The flexibility of this framework will make it possible to investigate the rules underlying axon growth and regeneration in the context of various neuronal populations.
MeSH term(s)	Algorithms ; Animals ; Axons/physiology ; Brain/cytology ; Brain/physiology ; Computational Biology ; Computer Simulation ; Drosophila melanogaster/cytology ; Drosophila melanogaster/genetics ; Drosophila melanogaster/physiology ; Imaging, Three-Dimensional ; Models, Neurological ; Mushroom Bodies/cytology ; Mushroom Bodies/physiology ; Mutation ; Nerve Regeneration/physiology ; Neurogenesis/genetics ; Neurogenesis/physiology ; Neurons/physiology ; Phenotype ; Stochastic Processes
Language	English
Publishing date	2018-12-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1006627
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Article ; Online: Embryo-scale epithelial buckling forms a propagating furrow that initiates gastrulation.

Fierling, Julien / John, Alphy / Delorme, Barthélémy / Torzynski, Alexandre / Blanchard, Guy B / Lye, Claire M / Popkova, Anna / Malandain, Grégoire / Sanson, Bénédicte / Étienne, Jocelyn / Marmottant, Philippe / Quilliet, Catherine / Rauzi, Matteo

Nature communications

2022 Volume 13, Issue 1, Page(s) 3348

Abstract: Cell apical constriction driven by actomyosin contraction forces is a conserved mechanism during tissue folding in embryo development. While much is now understood of the molecular mechanism responsible for apical constriction and of the tissue-scale ... ...

Abstract	Cell apical constriction driven by actomyosin contraction forces is a conserved mechanism during tissue folding in embryo development. While much is now understood of the molecular mechanism responsible for apical constriction and of the tissue-scale integration of the ensuing in-plane deformations, it is still not clear if apical actomyosin contraction forces are necessary or sufficient per se to drive tissue folding. To tackle this question, we use the Drosophila embryo model system that forms a furrow on the ventral side, initiating mesoderm internalization. Past computational models support the idea that cell apical contraction forces may not be sufficient and that active or passive cell apico-basal forces may be necessary to drive cell wedging leading to tissue furrowing. By using 3D computational modelling and in toto embryo image analysis and manipulation, we now challenge this idea and show that embryo-scale force balance at the tissue surface, rather than cell-autonomous shape changes, is necessary and sufficient to drive a buckling of the epithelial surface forming a furrow which propagates and initiates embryo gastrulation.
MeSH term(s)	Actomyosin/metabolism ; Animals ; Cell Shape ; Drosophila ; Drosophila melanogaster ; Embryo, Nonmammalian/metabolism ; Embryonic Development ; Gastrulation ; Morphogenesis
Chemical Substances	Actomyosin (9013-26-7)
Language	English
Publishing date	2022-06-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-30493-3
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Article ; Online: A tree-topology preserving pairing for 3D/2D registration.

Benseghir, Thomas / Malandain, Grégoire / Vaillant, Régis

International journal of computer assisted radiology and surgery

2015 Volume 10, Issue 6, Page(s) 913–923

Abstract: Purpose: Fusing preoperative and intra-operative information into a single space aims at taking advantage of two complementary modalities and necessitates a step of registration that must provide good alignment and relevant correspondences. This paper ... ...

Abstract	Purpose: Fusing preoperative and intra-operative information into a single space aims at taking advantage of two complementary modalities and necessitates a step of registration that must provide good alignment and relevant correspondences. This paper addresses both purposes in the case of 3D/2D vessel tree matching. Method: We propose a registration algorithm endorsing this vascular tree nature by providing a pairing procedure that preserves the tree topology and by integrating this pairing into an iterative algorithm maintaining pairing coherence. In addition, we define two complementary error measures quantifying the resulting alignment error and pairing error, and both are based on manual ground-truth that is independent of the type of transformation to retrieve. Results: Experiments were conducted on a database of 63 clinical cases, evaluating robustness and accuracy of our approach with respect to the iterative closest point algorithm. Conclusion: The proposed method exhibits good results in terms of both pairing and alignment as well as low sensitivity to rotations to be compensated (up to 30°).
MeSH term(s)	Algorithms ; Databases, Factual ; Humans ; Imaging, Three-Dimensional/methods ; Sensitivity and Specificity
Language	English
Publishing date	2015-06
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2365628-1
ISSN	1861-6429 ; 1861-6410
ISSN (online)	1861-6429
ISSN	1861-6410
DOI	10.1007/s11548-015-1207-0
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Article: Iterative closest curve: a framework for curvilinear structure registration application to 2D/3D coronary arteries registration.

Benseghir, Thomas / Malandain, Grégoire / Vaillant, Régis

Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention

2014 Volume 16, Issue Pt 1, Page(s) 179–186

Abstract: Treatment coronary arteries endovascular involves catheter navigation through patient vasculature. The projective angiography guidance is limited in the case of chronic total occlusion where occluded vessel can not be seen. Integrating standard ... ...

Abstract	Treatment coronary arteries endovascular involves catheter navigation through patient vasculature. The projective angiography guidance is limited in the case of chronic total occlusion where occluded vessel can not be seen. Integrating standard preoperative CT angiography information with live fluoroscopic images addresses this limitation but requires alignment of both modalities. This article proposes a structure-based registration method that intrinsically preserves both the geometrical and topological coherencies of the vascular centrelines to be registered, by the means of a dedicated curve-to-curve distance pairs of closest curves are identified, while pairing their points. Preliminary experiments demonstrate that the proposed approach performs better than the standard Iterative Closest Point method giving a wider attraction basin and improved accuracy.
MeSH term(s)	Algorithms ; Coronary Angiography/methods ; Coronary Artery Disease/diagnostic imaging ; Coronary Artery Disease/surgery ; Humans ; Imaging, Three-Dimensional/methods ; Pattern Recognition, Automated/methods ; Preoperative Care/methods ; Radiographic Image Enhancement/methods ; Radiographic Image Interpretation, Computer-Assisted/methods ; Reproducibility of Results ; Sensitivity and Specificity ; Subtraction Technique ; Surgery, Computer-Assisted/methods ; Tomography, X-Ray Computed/methods
Language	English
Publishing date	2014-01-30
Publishing country	Germany
Document type	Journal Article
DOI	10.1007/978-3-642-40811-3_23
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Article ; Online: Assessing the ability of the 2D Fisher-KPP equation to model cell-sheet wound closure.

Habbal, Abderrahmane / Barelli, Hélène / Malandain, Grégoire

Mathematical biosciences

2014 Volume 252, Page(s) 45–59

Abstract: We address in this paper the ability of the Fisher-KPP equations to render some of the dynamical features of epithelial cell-sheets during wound closure. Our approach is based on nonlinear parameter identification, in a two-dimensional setting, and using ...

Abstract	We address in this paper the ability of the Fisher-KPP equations to render some of the dynamical features of epithelial cell-sheets during wound closure. Our approach is based on nonlinear parameter identification, in a two-dimensional setting, and using advanced 2D image processing of the video acquired sequences. As original contribution, we lead a detailed study of the profiles of the classically used cost functions, and we address the "wound constant speed" assumption, showing that it should be handled with care. We study five MDCK cell monolayer assays in a reference, activated and inhibited migration conditions. Modulo the inherent variability of biological assays, we show that in the assay where migration is not exogeneously activated or inhibited, the wound velocity is constant. The Fisher-KPP equation is able to accurately predict, until the final closure of the wound, the evolution of the wound area, the mean velocity of the cell front, and the time at which the closure occurred. We also show that for activated as well as for inhibited migration assays, many of the cell-sheet dynamics cannot be well captured by the Fisher-KPP model. Finally, we draw some conclusions related to the identified model parameters, and possible utilization of the model.
MeSH term(s)	Animals ; Cell Movement/physiology ; Dogs ; Epithelial Cells/physiology ; Image Processing, Computer-Assisted ; Madin Darby Canine Kidney Cells ; Models, Biological ; Video Recording ; Wound Healing/physiology
Language	English
Publishing date	2014-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	1126-5
ISSN	1879-3134 ; 0025-5564
ISSN (online)	1879-3134
ISSN	0025-5564
DOI	10.1016/j.mbs.2014.03.009
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Article: The HV3 Score: A New Simple Tool to Suspect Cognitive Impairment in Multiple Sclerosis in Clinical Practice.

Laffon, Muriel / Malandain, Grégoire / Joly, Heloise / Cohen, Mikael / Lebrun, Christine

Neurology and therapy

2014 Volume 3, Issue 2, Page(s) 113–122

Abstract: Introduction: Cognitive impairment in multiple sclerosis (MS) is common even in the early stages of the disease. Our objective was to improve early detection of cognitive impairment in MS.: Methods: Seventy-five patients with relapsing remitting (RR) ...

Abstract	Introduction: Cognitive impairment in multiple sclerosis (MS) is common even in the early stages of the disease. Our objective was to improve early detection of cognitive impairment in MS. Methods: Seventy-five patients with relapsing remitting (RR) MS and 20 controls were enrolled. Two RRMS groups were defined according to their results at the Paced Auditory Serial Addition Test (PASAT). Patients with a z score below two standard deviations were considered impaired. We quantified T2 and T1 lesion volumes, and cerebral white and grey matter volumes on a conventional brain magnetic resonance imaging (MRI) scan. Global brain atrophy was evaluated using the third ventricle (V3) width (in mm). An average brain model was built based on controls and compared with the patient's MRI to quantify regional volumetric changes. Results: Sixteen (21.3%) patients with RRMS had low PASAT performance. They had a higher Expanded Disability Status Scale (EDSS) score (P = 0.019). T2 and T1 lesion volumes, and grey and white matter volumes were the same in both groups. An enlargement of the V3 width was observed in the low performer group (P = 0.044) and V3 width was correlated with the PASAT score (r = -0.271; P = 0.021). A composite score, named HV3, was obtained by adding the EDSS and V3 width (in mm) and correlated with the PASAT (r = -0.325; P = 0.006). A cutoff HV3 score of over 5.5 identified patients with low PASAT performance, with a positive predictive value of 92.5% and an accuracy of 70.1%. Focal atrophy was detected in the supplementary motor area, the cingulate gyrus, the right thalamus, and the inferior parietal lobules of patients with lower PASAT performance. Conclusion: Specific brain morphological changes, including an enlargement of the V3 width, are associated with low PASAT performance in patients with RRMS. The HV3 score is an additional and complementary tool, accessible in clinical practice, to suspect easily cognitive impairment in patients with RRMS and to better identify patients requiring a complete cognitive assessment.
Language	English
Publishing date	2014-11-25
Publishing country	New Zealand
Document type	Journal Article
ISSN	2193-8253
ISSN	2193-8253
DOI	10.1007/s40120-014-0021-x
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Article: Efficient selection of the most similar image in a database for critical structures segmentation.

Commowick, Olivier / Malandain, Grégoire

Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention

2007 Volume 10, Issue Pt 2, Page(s) 203–210

Abstract: Radiotherapy planning needs accurate delineations of the critical structures. Atlas-based segmentation has been shown to be very efficient to delineate brain structures. However, the construction of an atlas from a dataset of images, particularly for the ...

Abstract	Radiotherapy planning needs accurate delineations of the critical structures. Atlas-based segmentation has been shown to be very efficient to delineate brain structures. However, the construction of an atlas from a dataset of images, particularly for the head and neck region, is very difficult due to the high variability of the images and can generate over-segmented structures in the atlas. To overcome this drawback, we present in this paper an alternative method to select as a template the image in a database that is the most similar to the patient to be segmented. This similarity is based on a distance between transformations. A major contribution is that we do not compute every patient-to-sample registration to find the most similar template, but only the registration of the patient towards an average image. This method has therefore the advantage of being computationally very efficient. We present a qualitative and quantitative comparison between the proposed method and a classical atlas-based segmentation method. This evaluation is performed on a subset of 45 patients using a Leave-One-Out method and shows a great improvement of the specificity of the results.
MeSH term(s)	Algorithms ; Artificial Intelligence ; Database Management Systems ; Databases, Factual ; Head and Neck Neoplasms/diagnosis ; Humans ; Image Enhancement/methods ; Image Interpretation, Computer-Assisted/methods ; Information Storage and Retrieval/methods ; Magnetic Resonance Imaging/methods ; Pattern Recognition, Automated/methods ; Reproducibility of Results ; Sensitivity and Specificity
Language	English
Publishing date	2007-11-16
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
DOI	10.1007/978-3-540-75759-7_25
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Article ; Online: Contact area-dependent cell communication and the morphological invariance of ascidian embryogenesis.

Guignard, Léo / Fiúza, Ulla-Maj / Leggio, Bruno / Laussu, Julien / Faure, Emmanuel / Michelin, Gaël / Biasuz, Kilian / Hufnagel, Lars / Malandain, Grégoire / Godin, Christophe / Lemaire, Patrick

Science (New York, N.Y.)

2020 Volume 369, Issue 6500

Abstract: Marine invertebrate ascidians display embryonic reproducibility: Their early embryonic cell lineages are considered invariant and are conserved between distantly related species, despite rapid genomic divergence. Here, we address the drivers of this ... ...

Abstract	Marine invertebrate ascidians display embryonic reproducibility: Their early embryonic cell lineages are considered invariant and are conserved between distantly related species, despite rapid genomic divergence. Here, we address the drivers of this reproducibility. We used light-sheet imaging and automated cell segmentation and tracking procedures to systematically quantify the behavior of individual cells every 2 minutes during
MeSH term(s)	Animals ; Cell Communication ; Cell Division ; Cell Tracking ; Reproduction ; Urochordata/cytology ; Urochordata/embryology
Language	English
Publishing date	2020-07-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.aar5663
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Article ; Online: A multiscale analysis of early flower development in Arabidopsis provides an integrated view of molecular regulation and growth control.

Refahi, Yassin / Zardilis, Argyris / Michelin, Gaël / Wightman, Raymond / Leggio, Bruno / Legrand, Jonathan / Faure, Emmanuel / Vachez, Laetitia / Armezzani, Alessia / Risson, Anne-Evodie / Zhao, Feng / Das, Pradeep / Prunet, Nathanaël / Meyerowitz, Elliot M / Godin, Christophe / Malandain, Grégoire / Jönsson, Henrik / Traas, Jan

Developmental cell

2021 Volume 56, Issue 4, Page(s) 540–556.e8

Abstract: We have analyzed the link between the gene regulation and growth during the early stages of flower development in Arabidopsis. Starting from time-lapse images, we generated a 4D atlas of early flower development, including cell lineage, cellular growth ... ...

Abstract	We have analyzed the link between the gene regulation and growth during the early stages of flower development in Arabidopsis. Starting from time-lapse images, we generated a 4D atlas of early flower development, including cell lineage, cellular growth rates, and the expression patterns of regulatory genes. This information was introduced in MorphoNet, a web-based platform. Using computational models, we found that the literature-based molecular network only explained a minority of the gene expression patterns. This was substantially improved by adding regulatory hypotheses for individual genes. Correlating growth with the combinatorial expression of multiple regulators led to a set of hypotheses for the action of individual genes in morphogenesis. This identified the central factor LEAFY as a potential regulator of heterogeneous growth, which was supported by quantifying growth patterns in a leafy mutant. By providing an integrated view, this atlas should represent a fundamental step toward mechanistic models of flower development.
MeSH term(s)	Arabidopsis/cytology ; Arabidopsis/genetics ; Arabidopsis/growth & development ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Body Patterning/genetics ; Cell Lineage/genetics ; Flowers/anatomy & histology ; Flowers/cytology ; Flowers/genetics ; Flowers/growth & development ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Plant ; Gene Regulatory Networks ; Genes, Plant ; Morphogenesis/genetics ; Mutation/genetics
Chemical Substances	Arabidopsis Proteins
Language	English
Publishing date	2021-02-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2054967-2
ISSN	1878-1551 ; 1534-5807
ISSN (online)	1878-1551
ISSN	1534-5807
DOI	10.1016/j.devcel.2021.01.019
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Article: Using Frankenstein's creature paradigm to build a patient specific atlas.

Commowick, Olivier / Warfield, Simon K / Malandain, Grégoire

Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention

2010 Volume 12, Issue Pt 2, Page(s) 993–1000

Abstract: Conformal radiotherapy planning needs accurate delineations of the critical structures. Atlas-based segmentation has been shown to be very efficient to delineate brain structures. It would therefore be very interesting to develop an atlas for the head ... ...

Abstract	Conformal radiotherapy planning needs accurate delineations of the critical structures. Atlas-based segmentation has been shown to be very efficient to delineate brain structures. It would therefore be very interesting to develop an atlas for the head and neck region where 7% of the cancers arise. However, the construction of an atlas in this region is very difficult due to the high variability of the anatomies. This can generate segmentation errors and over-segmented structures in the atlas. To overcome this drawback, we present an alternative method to build a template locally adapted to the patient's anatomy. This is done first by selecting in a database the images that are the most similar to the patient on predefined regions of interest, using on a distance between transformations. The first major contribution is that we do not compute every patient-to-image registration to find the most similar image, but only the registration of the patient towards an average image. This method is therefore computationally very efficient. The second major contribution is a novel method to use the selected images and the predefined regions to build a "Frankenstein's creature" for segmentation. We present a qualitative and quantitative comparison between the proposed method and a classical atlas-based segmentation method. This evaluation is performed on a subset of 58 patients among a database of 105 head and neck CT images and shows a great improvement of the specificity of the results.
MeSH term(s)	Algorithms ; Computer Simulation ; Head and Neck Neoplasms/diagnostic imaging ; Humans ; Imaging, Three-Dimensional/methods ; Models, Anatomic ; Pattern Recognition, Automated/methods ; Radiographic Image Enhancement/methods ; Radiographic Image Interpretation, Computer-Assisted/methods ; Reproducibility of Results ; Sensitivity and Specificity ; Subtraction Technique ; Tomography, X-Ray Computed/methods
Language	English
Publishing date	2010-04-27
Publishing country	Germany
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
DOI	10.1007/978-3-642-04271-3_120
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