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Franco-Barranco D, Lin Z, Jang WD, Wang X, Shen Q, Yin W, Fan Y, Li M, Chen C, Xiong Z, Xin R, Liu H, Chen H, Li Z, Zhao J, Chen X, Pape C, Conrad R, Nightingale L, de Folter J, Jones ML, Liu Y, Ziaei D, Huschauer S, Arganda-Carreras I, Pfister H, Wei D. Current Progress and Challenges in Large-Scale 3D Mitochondria Instance Segmentation. IEEE Trans Med Imaging 2023; 42:3956-3971. [PMID: 37768797 PMCID: PMC10753957 DOI: 10.1109/tmi.2023.3320497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
In this paper, we present the results of the MitoEM challenge on mitochondria 3D instance segmentation from electron microscopy images, organized in conjunction with the IEEE-ISBI 2021 conference. Our benchmark dataset consists of two large-scale 3D volumes, one from human and one from rat cortex tissue, which are 1,986 times larger than previously used datasets. At the time of paper submission, 257 participants had registered for the challenge, 14 teams had submitted their results, and six teams participated in the challenge workshop. Here, we present eight top-performing approaches from the challenge participants, along with our own baseline strategies. Posterior to the challenge, annotation errors in the ground truth were corrected without altering the final ranking. Additionally, we present a retrospective evaluation of the scoring system which revealed that: 1) challenge metric was permissive with the false positive predictions; and 2) size-based grouping of instances did not correctly categorize mitochondria of interest. Thus, we propose a new scoring system that better reflects the correctness of the segmentation results. Although several of the top methods are compared favorably to our own baselines, substantial errors remain unsolved for mitochondria with challenging morphologies. Thus, the challenge remains open for submission and automatic evaluation, with all volumes available for download.
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Affiliation(s)
- Daniel Franco-Barranco
- Department of Computer Science and Artificial Intelligence, University of the Basque Country (UPV/EHU), 20018 San Sebastián, Spain, and also with the Donostia International Physics Center (DIPC), 20018 San Sebastián, Spain
| | - Zudi Lin
- Harvard John A. Paulson School of Engineering and Applied Sciences (SEAS), Harvard University, Allston, MA 02134 USA
| | - Won-Dong Jang
- Harvard John A. Paulson School of Engineering and Applied Sciences (SEAS), Harvard University, Allston, MA 02134 USA
| | - Xueying Wang
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
| | - Qijia Shen
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, OX3 9DU Oxford, U.K
| | - Wenjie Yin
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
| | - Yutian Fan
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
| | - Mingxing Li
- Department of Electronic Engineering and Information Science (EEIS), University of Science and Technology of China, Anhui 230026, China
| | - Chang Chen
- Department of Electronic Engineering and Information Science (EEIS), University of Science and Technology of China, Anhui 230026, China
| | - Zhiwei Xiong
- Department of Electronic Engineering and Information Science (EEIS), University of Science and Technology of China, Anhui 230026, China
| | - Rui Xin
- Institute of Image Processing and Pattern Recognition, Department of Automation, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Liu
- Institute of Image Processing and Pattern Recognition, Department of Automation, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huai Chen
- Institute of Image Processing and Pattern Recognition, Department of Automation, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhili Li
- National Engineering Laboratory for Brain-Inspired Intelligence Technology and Application, University of Science and Technology of China, Anhui 230026, China
| | - Jie Zhao
- National Engineering Laboratory for Brain-Inspired Intelligence Technology and Application, University of Science and Technology of China, Anhui 230026, China
| | - Xuejin Chen
- National Engineering Laboratory for Brain-Inspired Intelligence Technology and Application, University of Science and Technology of China, Anhui 230026, China
| | - Constantin Pape
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany. He is now with the Institute for Computer Science, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Ryan Conrad
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA, and also with the Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701 USA
| | | | | | | | - Yanling Liu
- Advanced Biomedical Computational Science Group, Frederick National Laboratory for Cancer Research, Frederick, MD 21701 USA
| | - Dorsa Ziaei
- Advanced Biomedical Computational Science Group, Frederick National Laboratory for Cancer Research, Frederick, MD 21701 USA
| | | | - Ignacio Arganda-Carreras
- Department of Computer Science and Artificial Intelligence, University of the Basque Country (UPV/EHU), 20018 San Sebastián, Spain, also with the Donostia International Physics Center (DIPC), 20018 San Sebastián, Spain, also with the IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain, and also with the Biofisika Institute, 48940 Leioa, Spain
| | - Hanspeter Pfister
- Harvard John A. Paulson School of Engineering and Applied Sciences (SEAS), Harvard University, Allston, MA 02134 USA
| | - Donglai Wei
- Computer Science Department, Boston College, Chestnut Hill, MA 02467 USA
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2
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Andrés-San Román JA, Gordillo-Vázquez C, Franco-Barranco D, Morato L, Fernández-Espartero CH, Baonza G, Tagua A, Vicente-Munuera P, Palacios AM, Gavilán MP, Martín-Belmonte F, Annese V, Gómez-Gálvez P, Arganda-Carreras I, Escudero LM. CartoCell, a high-content pipeline for 3D image analysis, unveils cell morphology patterns in epithelia. Cell Rep Methods 2023; 3:100597. [PMID: 37751739 PMCID: PMC10626192 DOI: 10.1016/j.crmeth.2023.100597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 07/19/2023] [Accepted: 08/31/2023] [Indexed: 09/28/2023]
Abstract
Decades of research have not yet fully explained the mechanisms of epithelial self-organization and 3D packing. Single-cell analysis of large 3D epithelial libraries is crucial for understanding the assembly and function of whole tissues. Combining 3D epithelial imaging with advanced deep-learning segmentation methods is essential for enabling this high-content analysis. We introduce CartoCell, a deep-learning-based pipeline that uses small datasets to generate accurate labels for hundreds of whole 3D epithelial cysts. Our method detects the realistic morphology of epithelial cells and their contacts in the 3D structure of the tissue. CartoCell enables the quantification of geometric and packing features at the cellular level. Our single-cell cartography approach then maps the distribution of these features on 2D plots and 3D surface maps, revealing cell morphology patterns in epithelial cysts. Additionally, we show that CartoCell can be adapted to other types of epithelial tissues.
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Affiliation(s)
- Jesús A Andrés-San Román
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | - Carmen Gordillo-Vázquez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | - Daniel Franco-Barranco
- Department of Computer Science and Artificial Intelligence, University of the Basque Country (UPV/EHU), 20018 San Sebastian, Spain; Donostia International Physics Center (DIPC), 20018 San Sebastian, Spain
| | - Laura Morato
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | - Cecilia H Fernández-Espartero
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | - Gabriel Baonza
- Program of Tissue and Organ Homeostasis, Centro de Biología Molecular Severo Ochoa, CSIC-UAM and Ramón & Cajal Health Research Institute (IRYCIS), Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | - Antonio Tagua
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | | | - Ana M Palacios
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | - María P Gavilán
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), JA/CSIC/Universidad de Sevilla/Universidad Pablo de Olavide and Departamento de Citología e Histología Normal y Patológica, Facultad de Medicina, Universidad de Sevilla, 41009 Seville, Spain
| | - Fernando Martín-Belmonte
- Program of Tissue and Organ Homeostasis, Centro de Biología Molecular Severo Ochoa, CSIC-UAM and Ramón & Cajal Health Research Institute (IRYCIS), Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | - Valentina Annese
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | - Pedro Gómez-Gálvez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain; MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Trumpington, Cambridge CB2 0QH, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK.
| | - Ignacio Arganda-Carreras
- Department of Computer Science and Artificial Intelligence, University of the Basque Country (UPV/EHU), 20018 San Sebastian, Spain; Donostia International Physics Center (DIPC), 20018 San Sebastian, Spain; Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain; Biofisika Institute, 48940 Leioa, Spain.
| | - Luis M Escudero
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), 28029 Madrid, Spain.
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Lauenburg L, Lin Z, Zhang R, Santos MD, Huang S, Arganda-Carreras I, Boyden ES, Pfister H, Wei D. 3D Domain Adaptive Instance Segmentation via Cyclic Segmentation GANs. IEEE J Biomed Health Inform 2023; 27:4018-4027. [PMID: 37252868 PMCID: PMC10481620 DOI: 10.1109/jbhi.2023.3281332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
3D instance segmentation for unlabeled imaging modalities is a challenging but essential task as collecting expert annotation can be expensive and time-consuming. Existing works segment a new modality by either deploying pre-trained models optimized on diverse training data or sequentially conducting image translation and segmentation with two relatively independent networks. In this work, we propose a novel Cyclic Segmentation Generative Adversarial Network (CySGAN) that conducts image translation and instance segmentation simultaneously using a unified network with weight sharing. Since the image translation layer can be removed at inference time, our proposed model does not introduce additional computational cost upon a standard segmentation model. For optimizing CySGAN, besides the CycleGAN losses for image translation and supervised losses for the annotated source domain, we also utilize self-supervised and segmentation-based adversarial objectives to enhance the model performance by leveraging unlabeled target domain images. We benchmark our approach on the task of 3D neuronal nuclei segmentation with annotated electron microscopy (EM) images and unlabeled expansion microscopy (ExM) data. The proposed CySGAN outperforms pre-trained generalist models, feature-level domain adaptation models, and the baselines that conduct image translation and segmentation sequentially. Our implementation and the newly collected, densely annotated ExM zebrafish brain nuclei dataset, named NucExM, are publicly available at https://connectomics-bazaar.github.io/proj/CySGAN/index.html.
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Gómez-Gálvez P, Vicente-Munuera P, Anbari S, Tagua A, Gordillo-Vázquez C, Andrés-San Román JA, Franco-Barranco D, Palacios AM, Velasco A, Capitán-Agudo C, Grima C, Annese V, Arganda-Carreras I, Robles R, Márquez A, Buceta J, Escudero LM. A quantitative biophysical principle to explain the 3D cellular connectivity in curved epithelia. Cell Syst 2022; 13:631-643.e8. [PMID: 35835108 DOI: 10.1016/j.cels.2022.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 02/15/2022] [Accepted: 06/15/2022] [Indexed: 01/26/2023]
Abstract
Epithelial cell organization and the mechanical stability of tissues are closely related. In this context, it has been recently shown that packing optimization in bended or folded epithelia is achieved by an energy minimization mechanism that leads to a complex cellular shape: the "scutoid". Here, we focus on the relationship between this shape and the connectivity between cells. We use a combination of computational, experimental, and biophysical approaches to examine how energy drivers affect the three-dimensional (3D) packing of tubular epithelia. We propose an energy-based stochastic model that explains the 3D cellular connectivity. Then, we challenge it by experimentally reducing the cell adhesion. As a result, we observed an increment in the appearance of scutoids that correlated with a decrease in the energy barrier necessary to connect with new cells. We conclude that tubular epithelia satisfy a quantitative biophysical principle that links tissue geometry and energetics with the average cellular connectivity.
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Affiliation(s)
- Pedro Gómez-Gálvez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain.
| | - Pablo Vicente-Munuera
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Samira Anbari
- Chemical and Biomolecular Engineering Department, Lehigh University, Bethlehem, PA 18018, USA
| | - Antonio Tagua
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Carmen Gordillo-Vázquez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Jesús A Andrés-San Román
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Daniel Franco-Barranco
- Department of Computer Science and Artificial Intelligence, University of the Basque Country (UPV/EHU), San Sebastian, Spain; Donostia International Physics Center (DIPC), San Sebastian, Spain
| | - Ana M Palacios
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Antonio Velasco
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain
| | - Carlos Capitán-Agudo
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain
| | - Clara Grima
- Departamento de Matemática Aplicada I, Universidad de Sevilla, Seville 41012, Spain
| | - Valentina Annese
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Ignacio Arganda-Carreras
- Department of Computer Science and Artificial Intelligence, University of the Basque Country (UPV/EHU), San Sebastian, Spain; Donostia International Physics Center (DIPC), San Sebastian, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Rafael Robles
- Departamento de Matemática Aplicada I, Universidad de Sevilla, Seville 41012, Spain
| | - Alberto Márquez
- Departamento de Matemática Aplicada I, Universidad de Sevilla, Seville 41012, Spain
| | - Javier Buceta
- Institute for Integrative Systems Biology (I2SysBio), CSIC-UV, Paterna 46980, Spain.
| | - Luis M Escudero
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain.
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5
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Franco-Barranco D, Pastor-Tronch J, González-Marfil A, Muñoz-Barrutia A, Arganda-Carreras I. Deep learning based domain adaptation for mitochondria segmentation on EM volumes. Comput Methods Programs Biomed 2022; 222:106949. [PMID: 35753105 DOI: 10.1016/j.cmpb.2022.106949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/05/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND OBJECTIVE Accurate segmentation of electron microscopy (EM) volumes of the brain is essential to characterize neuronal structures at a cell or organelle level. While supervised deep learning methods have led to major breakthroughs in that direction during the past years, they usually require large amounts of annotated data to be trained, and perform poorly on other data acquired under similar experimental and imaging conditions. This is a problem known as domain adaptation, since models that learned from a sample distribution (or source domain) struggle to maintain their performance on samples extracted from a different distribution or target domain. In this work, we address the complex case of deep learning based domain adaptation for mitochondria segmentation across EM datasets from different tissues and species. METHODS We present three unsupervised domain adaptation strategies to improve mitochondria segmentation in the target domain based on (1) state-of-the-art style transfer between images of both domains; (2) self-supervised learning to pre-train a model using unlabeled source and target images, and then fine-tune it only with the source labels; and (3) multi-task neural network architectures trained end-to-end with both labeled and unlabeled images. Additionally, to ensure good generalization in our models, we propose a new training stopping criterion based on morphological priors obtained exclusively in the source domain. The code and its documentation are publicly available at https://github.com/danifranco/EM_domain_adaptation. RESULTS We carried out all possible cross-dataset experiments using three publicly available EM datasets. We evaluated our proposed strategies and those of others based on the mitochondria semantic labels predicted on the target datasets. CONCLUSIONS The methods introduced here outperform the baseline methods and compare favorably to the state of the art. In the absence of validation labels, monitoring our proposed morphology-based metric is an intuitive and effective way to stop the training process and select in average optimal models.
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Affiliation(s)
- Daniel Franco-Barranco
- Dept. of Computer Science and Artificial Intelligence, University of the Basque Country (UPV/EHU), Spain; Donostia International Physics Center (DIPC), Spain.
| | - Julio Pastor-Tronch
- Dept. of Computer Science and Artificial Intelligence, University of the Basque Country (UPV/EHU), Spain
| | - Aitor González-Marfil
- Dept. of Computer Science and Artificial Intelligence, University of the Basque Country (UPV/EHU), Spain
| | - Arrate Muñoz-Barrutia
- Universidad Carlos III de Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Spain
| | - Ignacio Arganda-Carreras
- Dept. of Computer Science and Artificial Intelligence, University of the Basque Country (UPV/EHU), Spain; Donostia International Physics Center (DIPC), Spain; Ikerbasque, Basque Foundation for Science, Spain
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6
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Lekunberri X, Ruiz J, Quincoces I, Dornaika F, Arganda-Carreras I, Fernandes JA. Identification and measurement of tropical tuna species in purse seiner catches using computer vision and deep learning. ECOL INFORM 2022. [DOI: 10.1016/j.ecoinf.2021.101495] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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7
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Chourrout M, Roux M, Boisvert C, Gislard C, Legland D, Arganda-Carreras I, Olivier C, Peyrin F, Boutin H, Rama N, Baron T, Meyronet D, Brun E, Rositi H, Wiart M, Chauveau F. Brain virtual histology with X-ray phase-contrast tomography Part II:3D morphologies of amyloid- β plaques in Alzheimer's disease models. Biomed Opt Express 2022; 13:1640-1653. [PMID: 35414980 PMCID: PMC8973161 DOI: 10.1364/boe.438890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 05/15/2023]
Abstract
While numerous transgenic mouse strains have been produced to model the formation of amyloid-β (Aβ) plaques in the brain, efficient methods for whole-brain 3D analysis of Aβ deposits have to be validated and standardized. Moreover, routine immunohistochemistry performed on brain slices precludes any shape analysis of Aβ plaques, or require complex procedures for serial acquisition and reconstruction. The present study shows how in-line (propagation-based) X-ray phase-contrast tomography (XPCT) combined with ethanol-induced brain sample dehydration enables hippocampus-wide detection and morphometric analysis of Aβ plaques. Performed in three distinct Alzheimer mouse strains, the proposed workflow identified differences in signal intensity and 3D shape parameters: 3xTg displayed a different type of Aβ plaques, with a larger volume and area, greater elongation, flatness and mean breadth, and more intense average signal than J20 and APP/PS1. As a label-free non-destructive technique, XPCT can be combined with standard immunohistochemistry. XPCT virtual histology could thus become instrumental in quantifying the 3D spreading and the morphological impact of seeding when studying prion-like properties of Aβ aggregates in animal models of Alzheimer's disease. This is Part II of a series of two articles reporting the value of in-line XPCT for virtual histology of the brain; Part I shows how in-line XPCT enables 3D myelin mapping in the whole rodent brain and in human autopsy brain tissue.
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Affiliation(s)
- Matthieu Chourrout
- Univ. Lyon, Lyon Neuroscience Research Center, CNRS UMR5292, Inserm U1028, Université Claude Bernard Lyon 1, Lyon, France
| | - Margaux Roux
- Univ. Lyon, Lyon Neuroscience Research Center, CNRS UMR5292, Inserm U1028, Université Claude Bernard Lyon 1, Lyon, France
| | - Carlie Boisvert
- Univ. Lyon, Lyon Neuroscience Research Center, CNRS UMR5292, Inserm U1028, Université Claude Bernard Lyon 1, Lyon, France
- Current affiliation: Faculty of Medicine, The Ottawa Hospital and University of Ottawa, Ottawa, Ontario, Canada
| | - Coralie Gislard
- Univ. Lyon, Lyon Neuroscience Research Center, CNRS UMR5292, Inserm U1028, Université Claude Bernard Lyon 1, Lyon, France
| | | | - Ignacio Arganda-Carreras
- University of the Basque Country (UPV/EHU), San Sebastian, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Donostia International Physics Center (DIPC), San Sebastian, Spain
| | - Cécile Olivier
- Univ. Lyon, CREATIS; CNRS UMR5220; INSERM U1044; INSA-Lyon; Univ. Lyon 1, Lyon, France
| | - Françoise Peyrin
- Univ. Lyon, CREATIS; CNRS UMR5220; INSERM U1044; INSA-Lyon; Univ. Lyon 1, Lyon, France
| | - Hervé Boutin
- Univ. Manchester, Faculty of Biology Medicine and Health, Wolfson Molecular Imaging Centre, Manchester, UK
| | - Nicolas Rama
- Univ. Lyon, CRCL; INSERM U1052; CNRS UMR5286; Univ. Lyon 1; Centre Léon Bérard, Lyon, France
| | | | | | - Emmanuel Brun
- Univ. Grenoble Alpes, Inserm UA07 Strobe Grenoble, France
| | - Hugo Rositi
- Univ. Clermont Auvergne, Institut Pascal; CNRS UMR 6602; SIGMA Clermont, Clermont-Ferrand, France
| | - Marlène Wiart
- Univ. Lyon, CarMeN Laboratory; INSERM U1060; INRA U1397; Hospices Civils de Lyon, Lyon, France
- CNRS, Lyon, France
- These authors contributed equally to this work
| | - Fabien Chauveau
- Univ. Lyon, Lyon Neuroscience Research Center, CNRS UMR5292, Inserm U1028, Université Claude Bernard Lyon 1, Lyon, France
- CNRS, Lyon, France
- These authors contributed equally to this work
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Arganda S, Arganda-Carreras I, Gordon DG, Hoadley AP, Pérez-Escudero A, Giurfa M, Traniello JFA. Statistical Atlases and Automatic Labeling Strategies to Accelerate the Analysis of Social Insect Brain Evolution. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.745707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Current methods used to quantify brain size and compartmental scaling relationships in studies of social insect brain evolution involve manual annotations of images from histological samples, confocal microscopy or other sources. This process is susceptible to human bias and error and requires time-consuming effort by expert annotators. Standardized brain atlases, constructed through 3D registration and automatic segmentation, surmount these issues while increasing throughput to robustly sample diverse morphological and behavioral phenotypes. Here we design and evaluate three strategies to construct statistical brain atlases, or templates, using ants as a model taxon. The first technique creates a template by registering multiple brains of the same species. Brain regions are manually annotated on the template, and the labels are transformed back to each individual brain to obtain an automatic annotation, or to any other brain aligned with the template. The second strategy also creates a template from multiple brain images but obtains labels as a consensus from multiple manual annotations of individual brains comprising the template. The third technique is based on a template comprising brains from multiple species and the consensus of their labels. We used volume similarity as a metric to evaluate the automatic segmentation produced by each method against the inter- and intra-individual variability of human expert annotators. We found that automatic and manual methods are equivalent in volume accuracy, making the template technique an extraordinary tool to accelerate data collection and reduce human bias in the study of the evolutionary neurobiology of ants and other insects.
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9
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10
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Almeida A, Bermejo U, Bilbao A, Azkune G, Aguilera U, Emaldi M, Dornaika F, Arganda-Carreras I. A Comparative Analysis of Human Behavior Prediction Approaches in Intelligent Environments. Sensors (Basel) 2022; 22:701. [PMID: 35161448 PMCID: PMC8838738 DOI: 10.3390/s22030701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/13/2022] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
Behavior modeling has multiple applications in the intelligent environment domain. It has been used in different tasks, such as the stratification of different pathologies, prediction of the user actions and activities, or modeling the energy usage. Specifically, behavior prediction can be used to forecast the future evolution of the users and to identify those behaviors that deviate from the expected conduct. In this paper, we propose the use of embeddings to represent the user actions, and study and compare several behavior prediction approaches. We test multiple model (LSTM, CNNs, GCNs, and transformers) architectures to ascertain the best approach to using embeddings for behavior modeling and also evaluate multiple embedding retrofitting approaches. To do so, we use the Kasteren dataset for intelligent environments, which is one of the most widely used datasets in the areas of activity recognition and behavior modeling.
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Affiliation(s)
- Aitor Almeida
- DeustoTech Institute of Technology, University of Deusto, Av. Universidades 24, 48007 Bilbao, Spain; (U.B.); (A.B.); (U.A.); (M.E.)
| | - Unai Bermejo
- DeustoTech Institute of Technology, University of Deusto, Av. Universidades 24, 48007 Bilbao, Spain; (U.B.); (A.B.); (U.A.); (M.E.)
| | - Aritz Bilbao
- DeustoTech Institute of Technology, University of Deusto, Av. Universidades 24, 48007 Bilbao, Spain; (U.B.); (A.B.); (U.A.); (M.E.)
| | - Gorka Azkune
- Department of Computer Science and Artificial Intelligence, University of the Basque Country, M. Lardizabal 1, 20008 Donostia, Spain; (G.A.); (F.D.)
| | - Unai Aguilera
- DeustoTech Institute of Technology, University of Deusto, Av. Universidades 24, 48007 Bilbao, Spain; (U.B.); (A.B.); (U.A.); (M.E.)
| | - Mikel Emaldi
- DeustoTech Institute of Technology, University of Deusto, Av. Universidades 24, 48007 Bilbao, Spain; (U.B.); (A.B.); (U.A.); (M.E.)
| | - Fadi Dornaika
- Department of Computer Science and Artificial Intelligence, University of the Basque Country, M. Lardizabal 1, 20008 Donostia, Spain; (G.A.); (F.D.)
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi, 5, 48009 Bilbao, Spain;
| | - Ignacio Arganda-Carreras
- Ikerbasque, Basque Foundation for Science, Plaza Euskadi, 5, 48009 Bilbao, Spain;
- Donostia International Physics Center (DIPC), Manuel Lardizabal 4, 20018 San Sebastian, Spain
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11
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Franco-Barranco D, Muñoz-Barrutia A, Arganda-Carreras I. Stable Deep Neural Network Architectures for Mitochondria Segmentation on Electron Microscopy Volumes. Neuroinformatics 2021; 20:437-450. [PMID: 34855126 PMCID: PMC9546980 DOI: 10.1007/s12021-021-09556-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2021] [Indexed: 11/29/2022]
Abstract
Electron microscopy (EM) allows the identification of intracellular organelles such as mitochondria, providing insights for clinical and scientific studies. In recent years, a number of novel deep learning architectures have been published reporting superior performance, or even human-level accuracy, compared to previous approaches on public mitochondria segmentation datasets. Unfortunately, many of these publications make neither the code nor the full training details public, leading to reproducibility issues and dubious model comparisons. Thus, following a recent code of best practices in the field, we present an extensive study of the state-of-the-art architectures and compare them to different variations of U-Net-like models for this task. To unveil the impact of architectural novelties, a common set of pre- and post-processing operations has been implemented and tested with each approach. Moreover, an exhaustive sweep of hyperparameters has been performed, running each configuration multiple times to measure their stability. Using this methodology, we found very stable architectures and training configurations that consistently obtain state-of-the-art results in the well-known EPFL Hippocampus mitochondria segmentation dataset and outperform all previous works on two other available datasets: Lucchi++ and Kasthuri++. The code and its documentation are publicly available at https://github.com/danifranco/EM_Image_Segmentation.
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Affiliation(s)
- Daniel Franco-Barranco
- Donostia International Physics Center (DIPC), Donostia-San Sebastián, Spain. .,Department of Computer Science and Artificial Intelligence, University of the Basque Country (UPV/EHU), Donostia-San Sebastian, Spain.
| | - Arrate Muñoz-Barrutia
- Universidad Carlos III de Madrid, Leganés, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Ignacio Arganda-Carreras
- Donostia International Physics Center (DIPC), Donostia-San Sebastián, Spain.,Department of Computer Science and Artificial Intelligence, University of the Basque Country (UPV/EHU), Donostia-San Sebastian, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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12
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Abstract
Deep learning algorithms are powerful tools to analyse, restore and transform bioimaging data, increasingly used in life sciences research. These approaches now outperform most other algorithms for a broad range of image analysis tasks. In particular, one of the promises of deep learning is the possibility to provide parameter-free, one-click data analysis achieving expert-level performances in a fraction of the time previously required. However, as with most new and upcoming technologies, the potential for inappropriate use is raising concerns among the biomedical research community. This perspective aims to provide a short overview of key concepts that we believe are important for researchers to consider when using deep learning for their microscopy studies. These comments are based on our own experience gained while optimising various deep learning tools for bioimage analysis and discussions with colleagues from both the developer and user community. In particular, we focus on describing how results obtained using deep learning can be validated and discuss what should, in our views, be considered when choosing a suitable tool. We also suggest what aspects of a deep learning analysis would need to be reported in publications to describe the use of such tools to guarantee that the work can be reproduced. We hope this perspective will foster further discussion between developers, image analysis specialists, users and journal editors to define adequate guidelines and ensure that this transformative technology is used appropriately.
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Affiliation(s)
- Romain F Laine
- MRC-Laboratory for Molecular Cell Biology, University College London, London, UK
- The Francis Crick Institute, London, UK
- Micrographia Bio, Translation and Innovation Hub, London, UK
| | - Ignacio Arganda-Carreras
- Computer Science and Artificial Intelligence Department, University of the Basque Country (UPV/EHU), San Sebastian, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Donostia International Physics Center (DIPC), San Sebastian, Spain
| | - Ricardo Henriques
- MRC-Laboratory for Molecular Cell Biology, University College London, London, UK
- The Francis Crick Institute, London, UK
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Guillaume Jacquemet
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
- Faculty of Science and Engineering, Biosciences, Åbo Akademi University, Turku, Finland.
- Turku Bioimaging, University of Turku and Åbo Akademi University, Turku, Finland.
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13
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Hammoudi K, Benhabiles H, Melkemi M, Dornaika F, Arganda-Carreras I, Collard D, Scherpereel A. Deep Learning on Chest X-ray Images to Detect and Evaluate Pneumonia Cases at the Era of COVID-19. J Med Syst 2021; 45:75. [PMID: 34101042 PMCID: PMC8185498 DOI: 10.1007/s10916-021-01745-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 05/11/2021] [Indexed: 11/26/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is an infectious disease with first symptoms similar to the flu. COVID-19 appeared first in China and very quickly spreads to the rest of the world, causing then the 2019-20 coronavirus pandemic. In many cases, this disease causes pneumonia. Since pulmonary infections can be observed through radiography images, this paper investigates deep learning methods for automatically analyzing query chest X-ray images with the hope to bring precision tools to health professionals towards screening the COVID-19 and diagnosing confirmed patients. In this context, training datasets, deep learning architectures and analysis strategies have been experimented from publicly open sets of chest X-ray images. Tailored deep learning models are proposed to detect pneumonia infection cases, notably viral cases. It is assumed that viral pneumonia cases detected during an epidemic COVID-19 context have a high probability to presume COVID-19 infections. Moreover, easy-to-apply health indicators are proposed for estimating infection status and predicting patient status from the detected pneumonia cases. Experimental results show possibilities of training deep learning models over publicly open sets of chest X-ray images towards screening viral pneumonia. Chest X-ray test images of COVID-19 infected patients are successfully diagnosed through detection models retained for their performances. The efficiency of proposed health indicators is highlighted through simulated scenarios of patients presenting infections and health problems by combining real and synthetic health data.
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Affiliation(s)
- Karim Hammoudi
- Department of Computer Science, IRIMAS, Université de Haute-Alsace, 68100 Mulhouse, France
- Université de Strasbourg, Strasbourg, France
| | - Halim Benhabiles
- UMR 8520 - IEMN - Institut d’Electronique de Microélectronique et de Nanotechnologie, Université Lille, CNRS, Centrale Lille, Université Polytechnique Hauts-de-France, Junia, F-59000 Lille, France
| | - Mahmoud Melkemi
- Department of Computer Science, IRIMAS, Université de Haute-Alsace, 68100 Mulhouse, France
- Université de Strasbourg, Strasbourg, France
| | - Fadi Dornaika
- Department of Computer Science & Artificial Intelligence, University of the Basque Country, 20018 San Sebastián, Spain
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| | - Ignacio Arganda-Carreras
- Department of Computer Science & Artificial Intelligence, University of the Basque Country, 20018 San Sebastián, Spain
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
- Donostia International Physics Center (DIPC), 20018 San Sebastian, Spain
| | - Dominique Collard
- LIMMS/CNRS-IIS UMI 2820, Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba Meguro Ku, Tokyo, 153-8505 Japan
- CNRS/IIS/COL/Lille 1 SMMiL-E Project, CNRS Délégation Nord-Pas-de-Calais et Picardie, 2 rue des Canonniers, Lille, Cedex 59046 France
| | - Arnaud Scherpereel
- Lille University Hospital (CHU Lille), French National Institute of Health and Medical Research (Inserm), University of Lille, U1189 - ONCO-THAI, 59000 Lille, France
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14
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Wei D, Lin Z, Franco-Barranco D, Wendt N, Liu X, Yin W, Huang X, Gupta A, Jang WD, Wang X, Arganda-Carreras I, Lichtman JW, Pfister H. MitoEM Dataset: Large-scale 3D Mitochondria Instance Segmentation from EM Images. Med Image Comput Comput Assist Interv 2020; 12265:66-76. [PMID: 33283212 PMCID: PMC7713709 DOI: 10.1007/978-3-030-59722-1_7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Electron microscopy (EM) allows the identification of intracellular organelles such as mitochondria, providing insights for clinical and scientific studies. However, public mitochondria segmentation datasets only contain hundreds of instances with simple shapes. It is unclear if existing methods achieving human-level accuracy on these small datasets are robust in practice. To this end, we introduce the MitoEM dataset, a 3D mitochondria instance segmentation dataset with two (30μm)3 volumes from human and rat cortices respectively, 3, 600× larger than previous benchmarks. With around 40K instances, we find a great diversity of mitochondria in terms of shape and density. For evaluation, we tailor the implementation of the average precision (AP) metric for 3D data with a 45× speedup. On MitoEM, we find existing instance segmentation methods often fail to correctly segment mitochondria with complex shapes or close contacts with other instances. Thus, our MitoEM dataset poses new challenges to the field. We release our code and data: https://donglaiw.github.io/page/mitoEM/index.html.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Ignacio Arganda-Carreras
- Donostia International Physics Center
- University of the Basque Country
- Ikerbasque, Basque Foundation for Science
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15
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Borovec J, Kybic J, Arganda-Carreras I, Sorokin DV, Bueno G, Khvostikov AV, Bakas S, Chang EIC, Heldmann S, Kartasalo K, Latonen L, Lotz J, Noga M, Pati S, Punithakumar K, Ruusuvuori P, Skalski A, Tahmasebi N, Valkonen M, Venet L, Wang Y, Weiss N, Wodzinski M, Xiang Y, Xu Y, Yan Y, Yushkevich P, Zhao S, Munoz-Barrutia A. ANHIR: Automatic Non-Rigid Histological Image Registration Challenge. IEEE Trans Med Imaging 2020; 39:3042-3052. [PMID: 32275587 PMCID: PMC7584382 DOI: 10.1109/tmi.2020.2986331] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Automatic Non-rigid Histological Image Registration (ANHIR) challenge was organized to compare the performance of image registration algorithms on several kinds of microscopy histology images in a fair and independent manner. We have assembled 8 datasets, containing 355 images with 18 different stains, resulting in 481 image pairs to be registered. Registration accuracy was evaluated using manually placed landmarks. In total, 256 teams registered for the challenge, 10 submitted the results, and 6 participated in the workshop. Here, we present the results of 7 well-performing methods from the challenge together with 6 well-known existing methods. The best methods used coarse but robust initial alignment, followed by non-rigid registration, used multiresolution, and were carefully tuned for the data at hand. They outperformed off-the-shelf methods, mostly by being more robust. The best methods could successfully register over 98% of all landmarks and their mean landmark registration accuracy (TRE) was 0.44% of the image diagonal. The challenge remains open to submissions and all images are available for download.
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16
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Perez-Alvarez A, Fearey BC, O'Toole RJ, Yang W, Arganda-Carreras I, Lamothe-Molina PJ, Moeyaert B, Mohr MA, Panzera LC, Schulze C, Schreiter ER, Wiegert JS, Gee CE, Hoppa MB, Oertner TG. Freeze-frame imaging of synaptic activity using SynTagMA. Nat Commun 2020; 11:2464. [PMID: 32424147 PMCID: PMC7235013 DOI: 10.1038/s41467-020-16315-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 04/23/2020] [Indexed: 12/16/2022] Open
Abstract
Information within the brain travels from neuron to neuron across billions of synapses. At any given moment, only a small subset of neurons and synapses are active, but finding the active synapses in brain tissue has been a technical challenge. Here we introduce SynTagMA to tag active synapses in a user-defined time window. Upon 395-405 nm illumination, this genetically encoded marker of activity converts from green to red fluorescence if, and only if, it is bound to calcium. Targeted to presynaptic terminals, preSynTagMA allows discrimination between active and silent axons. Targeted to excitatory postsynapses, postSynTagMA creates a snapshot of synapses active just before photoconversion. To analyze large datasets, we show how to identify and track the fluorescence of thousands of individual synapses in an automated fashion. Together, these tools provide an efficient method for repeatedly mapping active neurons and synapses in cell culture, slice preparations, and in vivo during behavior.
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Affiliation(s)
- Alberto Perez-Alvarez
- Institute for Synaptic Physiology, University Medical Center Hamburg-Eppendorf, Hamburg, D-20251, Germany
| | - Brenna C Fearey
- Institute for Synaptic Physiology, University Medical Center Hamburg-Eppendorf, Hamburg, D-20251, Germany
| | - Ryan J O'Toole
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Wei Yang
- Research Group Synaptic Wiring and Information Processing, University Medical Center Hamburg-Eppendorf, Hamburg, D-20251, Germany
| | - Ignacio Arganda-Carreras
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Dept. of Computer Science and Artificial Intelligence, Basque Country University, San Sebastian, Spain
- Donostia International Physics Center (DIPC), San Sebastian, Spain
| | - Paul J Lamothe-Molina
- Institute for Synaptic Physiology, University Medical Center Hamburg-Eppendorf, Hamburg, D-20251, Germany
| | | | - Manuel A Mohr
- HHMI, Janelia Farm Research Campus, Ashburn, VA, 20147, USA
| | - Lauren C Panzera
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Christian Schulze
- Institute for Synaptic Physiology, University Medical Center Hamburg-Eppendorf, Hamburg, D-20251, Germany
| | | | - J Simon Wiegert
- Research Group Synaptic Wiring and Information Processing, University Medical Center Hamburg-Eppendorf, Hamburg, D-20251, Germany
| | - Christine E Gee
- Institute for Synaptic Physiology, University Medical Center Hamburg-Eppendorf, Hamburg, D-20251, Germany
| | - Michael B Hoppa
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Thomas G Oertner
- Institute for Synaptic Physiology, University Medical Center Hamburg-Eppendorf, Hamburg, D-20251, Germany.
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17
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Gómez-Olivencia A, López-Onaindia D, Sala N, Balzeau A, Pantoja-Pérez A, Arganda-Carreras I, Arlegi M, Rios-Garaizar J, Gómez-Robles A. The human remains from Axlor (Dima, Biscay, northern Iberian Peninsula). Am J Phys Anthropol 2019; 172:475-491. [PMID: 31889305 DOI: 10.1002/ajpa.23989] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/19/2019] [Accepted: 12/10/2019] [Indexed: 12/22/2022]
Abstract
OBJECTIVES We provide the description and comparative analysis of all the human fossil remains found at Axlor during the excavations carried out by J. M. de Barandiarán from 1967 to 1974: a cranial vault fragment and seven teeth, five of which likely belonged to the same individual, although two are currently lost. Our goal is to describe in detail all these human remains and discuss both their taxonomic attribution and their stratigraphic context. MATERIALS AND METHODS We describe external and internal anatomy, and use classic and geometric morphometrics. The teeth from Axlor are compared to Neandertals, Upper Paleolithic, and recent modern humans. RESULTS Two teeth (a left dm2 , a left di1 ) and the parietal fragment show morphological features consistent with a Neandertal classification, and were found in an undisturbed Mousterian context. The remaining three teeth (plus the two lost ones), initially classified as Neandertals, show morphological features and a general size that are more compatible with their classification as modern humans. DISCUSSION A left parietal fragment (Level VIII) from a single probably adult Neandertal individual was recovered during the old excavations performed by Barandiarán. Additionally, two different Neandertal children lost deciduous teeth during the formations of levels V (left di1 ) and IV (right dm2 ). In addition, a modern human individual is represented by five remains (two currently lost) from a complex stratigraphic setting. Some of the morphological features of these remains suggest that they may represent one of the scarce examples of Upper Paleolithic modern human remains in the northern Iberian Peninsula, which should be confirmed by direct dating.
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Affiliation(s)
- Asier Gómez-Olivencia
- Departamento de Estratigrafía y Paleontología, Facultad de Ciencia y Tecnología, Universidad del País Vasco-Euskal Herriko Unibertsitatea (UPV/EHU), Leioa, Spain.,IKERBASQUE. Basque Foundation for Science, Bilbao, Spain.,Sociedad de Ciencias Aranzadi, Donostia-San Sebastián, Spain.,Centro UCM-ISCIII de Investigación sobre Evolución y Comportamiento Humanos, Madrid, Spain
| | - Diego López-Onaindia
- GREAB, Unitat d'Antropologia Biològica, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facutat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Nohemi Sala
- Centro UCM-ISCIII de Investigación sobre Evolución y Comportamiento Humanos, Madrid, Spain.,Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Burgos, Spain
| | - Antoine Balzeau
- Équipe de Paléontologie Humaine, UMR 7194, CNRS, Département Homme et Environnement, Muséum National d'Histoire Naturelle, Musée de l'Homme, Paris, France.,Department of African Zoology, Royal Museum for Central Africa, Tervuren, Belgium
| | - Ana Pantoja-Pérez
- Centro UCM-ISCIII de Investigación sobre Evolución y Comportamiento Humanos, Madrid, Spain
| | - Ignacio Arganda-Carreras
- IKERBASQUE. Basque Foundation for Science, Bilbao, Spain.,Departamento de Ciencias de la Computacion e Inteligencia Artificial, Facultad de Informatica, Universidad del País Vasco-Euskal Herriko Unibertsitatea (UPV/EHU) Manuel Lardizabal Ibilbidea 1, Donostia-San Sebastián, Spain.,Donostia International Physics Center (DIPC), Manuel Lardizabal Ibilbidea 4, Donostia-San Sebastián, Spain
| | - Mikel Arlegi
- Departamento de Estratigrafía y Paleontología, Facultad de Ciencia y Tecnología, Universidad del País Vasco-Euskal Herriko Unibertsitatea (UPV/EHU), Leioa, Spain.,PACEA UMR 5199, Bâtiment B8, Allée Geoffroy Saint-Hilaire, Université de Bordeaux, Pessac, France
| | - Joseba Rios-Garaizar
- Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Burgos, Spain
| | - Aida Gómez-Robles
- Department of Anthropology, University College London, London, UK.,Department of Genetics, Evolution and Environment, University College London, London, UK.,Department of Life Sciences, Natural History Museum, London, UK
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18
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Gordon DG, Zelaya A, Arganda-Carreras I, Arganda S, Traniello JFA. Correction: Division of labor and brain evolution in insect societies: Neurobiology of extreme specialization in the turtle ant Cephalotes varians. PLoS One 2019; 14:e0219036. [PMID: 31233562 PMCID: PMC6590955 DOI: 10.1371/journal.pone.0219036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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19
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Gordon DG, Zelaya A, Arganda-Carreras I, Arganda S, Traniello JFA. Division of labor and brain evolution in insect societies: Neurobiology of extreme specialization in the turtle ant Cephalotes varians. PLoS One 2019; 14:e0213618. [PMID: 30917163 PMCID: PMC6436684 DOI: 10.1371/journal.pone.0213618] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 02/25/2019] [Indexed: 12/29/2022] Open
Abstract
Strongly polyphenic social insects provide excellent models to examine the neurobiological basis of division of labor. Turtle ants, Cephalotes varians, have distinct minor worker, soldier, and reproductive (gyne/queen) morphologies associated with their behavioral profiles: small-bodied task-generalist minors lack the phragmotic shield-shaped heads of soldiers, which are specialized to block and guard the nest entrance. Gynes found new colonies and during early stages of colony growth overlap behaviorally with soldiers. Here we describe patterns of brain structure and synaptic organization associated with division of labor in C. varians minor workers, soldiers, and gynes. We quantified brain volumes, determined scaling relationships among brain regions, and quantified the density and size of microglomeruli, synaptic complexes in the mushroom body calyxes important to higher-order processing abilities that may underpin behavioral performance. We found that brain volume was significantly larger in gynes; minor workers and soldiers had similar brain sizes. Consistent with their larger behavioral repertoire, minors had disproportionately larger mushroom bodies than soldiers and gynes. Soldiers and gynes had larger optic lobes, which may be important for flight and navigation in gynes, but serve different functions in soldiers. Microglomeruli were larger and less dense in minor workers; soldiers and gynes did not differ. Correspondence in brain structure despite differences in soldiers and gyne behavior may reflect developmental integration, suggesting that neurobiological metrics not only advance our understanding of brain evolution in social insects, but may also help resolve questions of the origin of novel castes.
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Affiliation(s)
- Darcy Greer Gordon
- Department of Biology, Boston University, Boston, MA, United States of America
- * E-mail:
| | - Alejandra Zelaya
- Department of Biology, Boston University, Boston, MA, United States of America
| | - Ignacio Arganda-Carreras
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Department of Computer Science and Artificial Intelligence, Basque Country University, San Sebastian, Spain
- Donostia International Physics Center (DIPC), San Sebastian, Spain
| | - Sara Arganda
- Department of Biology, Boston University, Boston, MA, United States of America
- Departamento de Biología y Geología, Física y Química Inorgánica, Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Madrid, Spain
| | - James F. A. Traniello
- Department of Biology, Boston University, Boston, MA, United States of America
- Graduate Program for Neuroscience, Boston University, Boston, MA, United States of America
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20
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Olazabal-Herrero A, Sendino M, Arganda-Carreras I, Rodríguez JA. WDR20 regulates shuttling of the USP12 deubiquitinase complex between the plasma membrane, cytoplasm and nucleus. Eur J Cell Biol 2019; 98:12-26. [PMID: 30466959 DOI: 10.1016/j.ejcb.2018.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 10/01/2018] [Accepted: 10/25/2018] [Indexed: 12/31/2022] Open
Abstract
The human deubiquitinases USP12 and USP46 are very closely related paralogs with critical functions as tumor suppressors. The catalytic activity of these enzymes is regulated by two cofactors: UAF1 and WDR20. USP12 and USP46 show nearly 90% amino acid sequence identity and share some cellular activities, but have also evolved non-overlapping functions. We hypothesized that, correlating with their functional divergence, the subcellular localization of USP12 and USP46 might be differentially regulated by their cofactors. We used confocal and live microscopy analyses of epitope-tagged proteins to determine the effect of UAF1 and WDR20 on the localization of USP12 and USP46. We found that WDR20 differently modulated the localization of the DUBs, promoting recruitment of USP12, but not USP46, to the plasma membrane. Using site-directed mutagenesis, we generated a large set of USP12 and WDR20 mutants to characterize in detail the mechanisms and sequence determinants that modulate the subcellular localization of the USP12/UAF1/WDR20 complex. Our data suggest that the USP12/UAF1/WDR20 complex dynamically shuttles between the plasma membrane, cytoplasm and nucleus. This shuttling involved active nuclear export mediated by the CRM1 pathway, and required a short N-terminal motif (1MEIL4) in USP12, as well as a novel nuclear export sequence (450MDGAIASGVSKFATLSLHD468) in WDR20. In conclusion, USP12 and USP46 have evolved divergently in terms of cofactor binding-regulated subcellular localization. WDR20 plays a crucial role in as a "targeting subunit" that modulates CRM1-dependent shuttling of the USP12/UAF1/WDR20 complex between the plasma membrane, cytoplasm and nucleus.
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Affiliation(s)
- Anne Olazabal-Herrero
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain
| | - Maria Sendino
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain
| | - Ignacio Arganda-Carreras
- Computer Science and Artificial Intelligence Department, University of the Basque Country (UPV/EHU), San Sebastian 20018, Spain; Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain; Donostia International Physics Center (DIPC), P. Manuel Lardizabal 4, 20018 San Sebastian, Spain
| | - Jose Antonio Rodríguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain.
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Arganda-Carreras I, Kaynig V, Rueden C, Eliceiri KW, Schindelin J, Cardona A, Sebastian Seung H. Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification. Bioinformatics 2018; 33:2424-2426. [PMID: 28369169 DOI: 10.1093/bioinformatics/btx180] [Citation(s) in RCA: 772] [Impact Index Per Article: 128.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 03/28/2017] [Indexed: 11/14/2022] Open
Abstract
Summary State-of-the-art light and electron microscopes are capable of acquiring large image datasets, but quantitatively evaluating the data often involves manually annotating structures of interest. This process is time-consuming and often a major bottleneck in the evaluation pipeline. To overcome this problem, we have introduced the Trainable Weka Segmentation (TWS), a machine learning tool that leverages a limited number of manual annotations in order to train a classifier and segment the remaining data automatically. In addition, TWS can provide unsupervised segmentation learning schemes (clustering) and can be customized to employ user-designed image features or classifiers. Availability and Implementation TWS is distributed as open-source software as part of the Fiji image processing distribution of ImageJ at http://imagej.net/Trainable_Weka_Segmentation . Contact ignacio.arganda@ehu.eus. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ignacio Arganda-Carreras
- Ikerbasque, Basque Foundation for Science, Bilbao 48013, Spain.,Computer Science and Artificial Intelligence Department, Basque Country University, San Sebastian 20018, Spain.,Donostia International Physics Center, San Sebastian 20018, Spain
| | - Verena Kaynig
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Curtis Rueden
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin, Madison, WI 53706, USA
| | - Kevin W Eliceiri
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin, Madison, WI 53706, USA
| | - Johannes Schindelin
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin, Madison, WI 53706, USA
| | - Albert Cardona
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - H Sebastian Seung
- Neuroscience Institute and Computer Science Department, Princeton University, NJ 08544, USA
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22
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Arganda-Carreras I, Manoliu T, Mazuras N, Schulze F, Iglesias JE, Bühler K, Jenett A, Rouyer F, Andrey P. A Statistically Representative Atlas for Mapping Neuronal Circuits in the Drosophila Adult Brain. Front Neuroinform 2018; 12:13. [PMID: 29628885 PMCID: PMC5876320 DOI: 10.3389/fninf.2018.00013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 03/01/2018] [Indexed: 11/13/2022] Open
Abstract
Imaging the expression patterns of reporter constructs is a powerful tool to dissect the neuronal circuits of perception and behavior in the adult brain of Drosophila, one of the major models for studying brain functions. To date, several Drosophila brain templates and digital atlases have been built to automatically analyze and compare collections of expression pattern images. However, there has been no systematic comparison of performances between alternative atlasing strategies and registration algorithms. Here, we objectively evaluated the performance of different strategies for building adult Drosophila brain templates and atlases. In addition, we used state-of-the-art registration algorithms to generate a new group-wise inter-sex atlas. Our results highlight the benefit of statistical atlases over individual ones and show that the newly proposed inter-sex atlas outperformed existing solutions for automated registration and annotation of expression patterns. Over 3,000 images from the Janelia Farm FlyLight collection were registered using the proposed strategy. These registered expression patterns can be searched and compared with a new version of the BrainBaseWeb system and BrainGazer software. We illustrate the validity of our methodology and brain atlas with registration-based predictions of expression patterns in a subset of clock neurons. The described registration framework should benefit to brain studies in Drosophila and other insect species.
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Affiliation(s)
- Ignacio Arganda-Carreras
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain.,Donostia International Physics Center, Donostia-San Sebastian, Spain
| | - Tudor Manoliu
- Institut des Neurosciences Paris-Saclay, Université Paris Sud, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Nicolas Mazuras
- Institut des Neurosciences Paris-Saclay, Université Paris Sud, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Florian Schulze
- VRVis Zentrum für Virtual Reality und Visualisierung Forschungs-GmbH, Vienna, Austria
| | - Juan E Iglesias
- Basque Center on Cognition, Brain and Language, Donostia-San Sebastian, Spain
| | - Katja Bühler
- VRVis Zentrum für Virtual Reality und Visualisierung Forschungs-GmbH, Vienna, Austria
| | - Arnim Jenett
- Tefor Core Facility, Institut des Neurosciences Paris-Saclay, Université Paris Sud, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - François Rouyer
- Institut des Neurosciences Paris-Saclay, Université Paris Sud, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Philippe Andrey
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
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23
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Malhan D, Muelke M, Rosch S, Schaefer AB, Merboth F, Weisweiler D, Heiss C, Arganda-Carreras I, El Khassawna T. An Optimized Approach to Perform Bone Histomorphometry. Front Endocrinol (Lausanne) 2018; 9:666. [PMID: 30519215 PMCID: PMC6259258 DOI: 10.3389/fendo.2018.00666] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 10/25/2018] [Indexed: 12/17/2022] Open
Abstract
Bone histomorphometry allows quantitative evaluation of bone micro-architecture, bone formation, and bone remodeling by providing an insight to cellular changes. Histomorphometry plays an important role in monitoring changes in bone properties because of systemic skeletal diseases like osteoporosis and osteomalacia. Besides, quantitative evaluation plays an important role in fracture healing studies to explore the effect of biomaterial or drug treatment. However, until today, to our knowledge, bone histomorphometry remain time-consuming and expensive. This incited us to set up an open-source freely available semi-automated solution to measure parameters like trabecular area, osteoid area, trabecular thickness, and osteoclast activity. Here in this study, the authors present the adaptation of Trainable Weka Segmentation plugin of ImageJ to allow fast evaluation of bone parameters (trabecular area, osteoid area) to diagnose bone related diseases. Also, ImageJ toolbox and plugins (BoneJ) were adapted to measure osteoclast activity, trabecular thickness, and trabecular separation. The optimized two different scripts are based on ImageJ, by providing simple user-interface and easy accessibility for biologists and clinicians. The scripts developed for bone histomorphometry can be optimized globally for other histological samples. The showed scripts will benefit the scientific community in histological evaluation.
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Affiliation(s)
- Deeksha Malhan
- Experimental Trauma Surgery, Faculty of Medicine, Justus-Liebig University of Giessen, Giessen, Germany
| | - Matthias Muelke
- Experimental Trauma Surgery, Faculty of Medicine, Justus-Liebig University of Giessen, Giessen, Germany
- Department of Trauma, Hand, and Reconstructive Surgery, University Hospital of Giessen and Marburg, Giessen, Germany
| | - Sebastian Rosch
- Experimental Trauma Surgery, Faculty of Medicine, Justus-Liebig University of Giessen, Giessen, Germany
| | - Annemarie B. Schaefer
- Experimental Trauma Surgery, Faculty of Medicine, Justus-Liebig University of Giessen, Giessen, Germany
| | - Felix Merboth
- Experimental Trauma Surgery, Faculty of Medicine, Justus-Liebig University of Giessen, Giessen, Germany
| | - David Weisweiler
- Experimental Trauma Surgery, Faculty of Medicine, Justus-Liebig University of Giessen, Giessen, Germany
- Department of Trauma, Hand, and Reconstructive Surgery, University Hospital of Giessen and Marburg, Giessen, Germany
| | - Christian Heiss
- Experimental Trauma Surgery, Faculty of Medicine, Justus-Liebig University of Giessen, Giessen, Germany
- Department of Trauma, Hand, and Reconstructive Surgery, University Hospital of Giessen and Marburg, Giessen, Germany
| | - Ignacio Arganda-Carreras
- Department of Computer Science and Artificial Intelligence, Basque Country University, San Sebastian, Spain
- *Correspondence: Ignacio Arganda-Carreras
| | - Thaqif El Khassawna
- Experimental Trauma Surgery, Faculty of Medicine, Justus-Liebig University of Giessen, Giessen, Germany
- Thaqif El Khassawna
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Abstract
With the progress of microscopy techniques and the rapidly growing amounts of acquired imaging data, there is an increased need for automated image processing and analysis solutions in biological studies. Each new application requires the design of a specific image analysis pipeline, by assembling a series of image processing operations. Many commercial or free bioimage analysis software are now available and several textbooks and reviews have presented the mathematical and computational fundamentals of image processing and analysis. Tens, if not hundreds, of algorithms and methods have been developed and integrated into image analysis software, resulting in a combinatorial explosion of possible image processing sequences. This paper presents a general guideline methodology to rationally address the design of image processing and analysis pipelines. The originality of the proposed approach is to follow an iterative, backwards procedure from the target objectives of analysis. The proposed goal-oriented strategy should help biologists to better apprehend image analysis in the context of their research and should allow them to efficiently interact with image processing specialists.
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Affiliation(s)
- Ignacio Arganda-Carreras
- Ikerbasque, Basque Foundation for Science, 48013, Bilbao, Spain
- Computer Science and Artificial Intelligence Department, Basque Country University (UPV/EHU), 20018, Donostia-San Sebastian, Spain
- Donostia International Physics Center (DIPC), 20018, Donostia-San Sebastian, Spain
| | - Philippe Andrey
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000, Versailles, France.
- Sorbonne Universités, UPMC Univ Paris 06, UFR 927, Paris, France.
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25
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Legland D, Arganda-Carreras I, Andrey P. MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ. Bioinformatics 2016; 32:3532-3534. [DOI: 10.1093/bioinformatics/btw413] [Citation(s) in RCA: 396] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/20/2016] [Accepted: 06/19/2016] [Indexed: 12/20/2022] Open
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26
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Arganda-Carreras I, Turaga SC, Berger DR, Cireşan D, Giusti A, Gambardella LM, Schmidhuber J, Laptev D, Dwivedi S, Buhmann JM, Liu T, Seyedhosseini M, Tasdizen T, Kamentsky L, Burget R, Uher V, Tan X, Sun C, Pham TD, Bas E, Uzunbas MG, Cardona A, Schindelin J, Seung HS. Crowdsourcing the creation of image segmentation algorithms for connectomics. Front Neuroanat 2015; 9:142. [PMID: 26594156 PMCID: PMC4633678 DOI: 10.3389/fnana.2015.00142] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/19/2015] [Indexed: 11/13/2022] Open
Abstract
To stimulate progress in automating the reconstruction of neural circuits, we organized the first international challenge on 2D segmentation of electron microscopic (EM) images of the brain. Participants submitted boundary maps predicted for a test set of images, and were scored based on their agreement with a consensus of human expert annotations. The winning team had no prior experience with EM images, and employed a convolutional network. This “deep learning” approach has since become accepted as a standard for segmentation of EM images. The challenge has continued to accept submissions, and the best so far has resulted from cooperation between two teams. The challenge has probably saturated, as algorithms cannot progress beyond limits set by ambiguities inherent in 2D scoring and the size of the test dataset. Retrospective evaluation of the challenge scoring system reveals that it was not sufficiently robust to variations in the widths of neurite borders. We propose a solution to this problem, which should be useful for a future 3D segmentation challenge.
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Affiliation(s)
- Ignacio Arganda-Carreras
- UMR1318 French National Institute for Agricultural Research-AgroParisTech, French National Institute for Agricultural Research Centre de Versailles-Grignon, Institut Jean-Pierre Bourgin Versailles, France
| | - Srinivas C Turaga
- Howard Hughes Medical Institute, Janelia Research Campus Ashburn, VA, USA
| | - Daniel R Berger
- Center for Brain Science, Harvard University Cambridge, MA, USA
| | - Dan Cireşan
- Swiss AI Lab IDSIA (Dalle Molle Institute for Artificial Intelligence) Universitá Della Svizzera Italiana, Scuola Universitaria Professionale Della Svizzera Italiana Lugano, Switzerland
| | - Alessandro Giusti
- Swiss AI Lab IDSIA (Dalle Molle Institute for Artificial Intelligence) Universitá Della Svizzera Italiana, Scuola Universitaria Professionale Della Svizzera Italiana Lugano, Switzerland
| | - Luca M Gambardella
- Swiss AI Lab IDSIA (Dalle Molle Institute for Artificial Intelligence) Universitá Della Svizzera Italiana, Scuola Universitaria Professionale Della Svizzera Italiana Lugano, Switzerland
| | - Jürgen Schmidhuber
- Swiss AI Lab IDSIA (Dalle Molle Institute for Artificial Intelligence) Universitá Della Svizzera Italiana, Scuola Universitaria Professionale Della Svizzera Italiana Lugano, Switzerland
| | - Dmitry Laptev
- Department of Computer Science, ETH Zurich Zurich, Switzerland
| | - Sarvesh Dwivedi
- Department of Computer Science, ETH Zurich Zurich, Switzerland
| | | | - Ting Liu
- Scientific Computing and Imaging Institute, University of Utah Salt Lake City, UT, USA
| | - Mojtaba Seyedhosseini
- Scientific Computing and Imaging Institute, University of Utah Salt Lake City, UT, USA
| | - Tolga Tasdizen
- Scientific Computing and Imaging Institute, University of Utah Salt Lake City, UT, USA
| | - Lee Kamentsky
- Imaging Platform, Broad Institute Cambridge, MA, USA
| | - Radim Burget
- Department of Telecommunications, Faculty of Electrical Engineering and Communication, Brno University of Technology Brno, Czech Republic
| | - Vaclav Uher
- Department of Telecommunications, Faculty of Electrical Engineering and Communication, Brno University of Technology Brno, Czech Republic
| | - Xiao Tan
- School of Engineering and Information Technology, University of New South Wales Canberra, ACT, Australia
| | - Changming Sun
- Digital Productivity Flagship, Commonwealth Scientific and Industrial Research Organisation North Ryde, NSW, Australia
| | - Tuan D Pham
- Department of Biomedical Engineering, The Institute of Technology, Linkoping University Linkoping, Sweden
| | - Erhan Bas
- Howard Hughes Medical Institute, Janelia Research Campus Ashburn, VA, USA
| | - Mustafa G Uzunbas
- Computer Science Department, Rutgers University New Brunswick, NJ, USA
| | - Albert Cardona
- Howard Hughes Medical Institute, Janelia Research Campus Ashburn, VA, USA
| | - Johannes Schindelin
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison Madison, WI, USA
| | - H Sebastian Seung
- Princeton Neuroscience Institute and Computer Science Department, Princeton University Princeton, NJ, USA
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27
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Cabrera J, Díaz-Manzano FE, Barcala M, Arganda-Carreras I, de Almeida-Engler J, Engler G, Fenoll C, Escobar C. Phenotyping nematode feeding sites: three-dimensional reconstruction and volumetric measurements of giant cells induced by root-knot nematodes in Arabidopsis. New Phytol 2015; 206:868-80. [PMID: 25613856 DOI: 10.1111/nph.13249] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 11/19/2014] [Indexed: 05/08/2023]
Abstract
The control of plant parasitic nematodes is an increasing problem. A key process during the infection is the induction of specialized nourishing cells, called giant cells (GCs), in roots. Understanding the function of genes required for GC development is crucial to identify targets for new control strategies. We propose a standardized method for GC phenotyping in different plant genotypes, like those with modified genes essential for GC development. The method combines images obtained by bright-field microscopy from the complete serial sectioning of galls with TrakEM2, specialized three-dimensional (3D) reconstruction software for biological structures. The volumes and shapes from 162 3D models of individual GCs induced by Meloidogyne javanica in Arabidopsis were analyzed for the first time along their life cycle. A high correlation between the combined volume of all GCs within a gall and the total area occupied by all the GCs in the section/s where they show maximum expansion, and a proof of concept from two Arabidopsis transgenic lines (J0121 ≫ DTA and J0121 ≫ GFP) demonstrate the reliability of the method. We phenotyped GCs and developed a reliable simplified method based on a two-dimensional (2D) parameter for comparison of GCs from different Arabidopsis genotypes, which is also applicable to galls from different plant species and in different growing conditions, as thickness/transparency is not a restriction.
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Affiliation(s)
- Javier Cabrera
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Av. Carlos III s/n, E-45071, Toledo, Spain
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28
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Kim Y, Venkataraju KU, Pradhan K, Mende C, Taranda J, Turaga SC, Arganda-Carreras I, Ng L, Hawrylycz MJ, Rockland KS, Seung HS, Osten P. Mapping social behavior-induced brain activation at cellular resolution in the mouse. Cell Rep 2014; 10:292-305. [PMID: 25558063 DOI: 10.1016/j.celrep.2014.12.014] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 10/21/2014] [Accepted: 12/05/2014] [Indexed: 12/22/2022] Open
Abstract
Understanding how brain activation mediates behaviors is a central goal of systems neuroscience. Here, we apply an automated method for mapping brain activation in the mouse in order to probe how sex-specific social behaviors are represented in the male brain. Our method uses the immediate-early-gene c-fos, a marker of neuronal activation, visualized by serial two-photon tomography: the c-fos-GFP+ neurons are computationally detected, their distribution is registered to a reference brain and a brain atlas, and their numbers are analyzed by statistical tests. Our results reveal distinct and shared female and male interaction-evoked patterns of male brain activation representing sex discrimination and social recognition. We also identify brain regions whose degree of activity correlates to specific features of social behaviors and estimate the total numbers and the densities of activated neurons per brain areas. Our study opens the door to automated screening of behavior-evoked brain activation in the mouse.
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Affiliation(s)
- Yongsoo Kim
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Kith Pradhan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Carolin Mende
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Julian Taranda
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Srinivas C Turaga
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Boston, MA 02139, USA
| | - Ignacio Arganda-Carreras
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Boston, MA 02139, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | | | - Kathleen S Rockland
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Boston University School of Medicine, Boston, MA 02118, USA
| | - H Sebastian Seung
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Boston, MA 02139, USA
| | - Pavel Osten
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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Poulet A, Arganda-Carreras I, Legland D, Probst AV, Andrey P, Tatout C. NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei. Bioinformatics 2014; 31:1144-6. [DOI: 10.1093/bioinformatics/btu774] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 11/14/2014] [Indexed: 11/12/2022] Open
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30
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Gul-Mohammed J, Arganda-Carreras I, Andrey P, Galy V, Boudier T. A generic classification-based method for segmentation of nuclei in 3D images of early embryos. BMC Bioinformatics 2014; 15:9. [PMID: 24423252 PMCID: PMC3900670 DOI: 10.1186/1471-2105-15-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 12/23/2013] [Indexed: 11/10/2022] Open
Abstract
Background Studying how individual cells spatially and temporally organize within the embryo is a fundamental issue in modern developmental biology to better understand the first stages of embryogenesis. In order to perform high-throughput analyses in three-dimensional microscopic images, it is essential to be able to automatically segment, classify and track cell nuclei. Many 3D/4D segmentation and tracking algorithms have been reported in the literature. Most of them are specific to particular models or acquisition systems and often require the fine tuning of parameters. Results We present a new automatic algorithm to segment and simultaneously classify cell nuclei in 3D/4D images. Segmentation relies on training samples that are interactively provided by the user and on an iterative thresholding process. This algorithm can correctly segment nuclei even when they are touching, and remains effective under temporal and spatial intensity variations. The segmentation is coupled to a classification of nuclei according to cell cycle phases, allowing biologists to quantify the effect of genetic perturbations and drug treatments. Robust 3D geometrical shape descriptors are used as training features for classification. Segmentation and classification results of three complete datasets are presented. In our working dataset of the Caenorhabditis elegans embryo, only 21 nuclei out of 3,585 were not detected, the overall F-score for segmentation reached 0.99, and more than 95% of the nuclei were classified in the correct cell cycle phase. No merging of nuclei was found. Conclusion We developed a novel generic algorithm for segmentation and classification in 3D images. The method, referred to as Adaptive Generic Iterative Thresholding Algorithm (AGITA), is freely available as an ImageJ plug-in.
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Affiliation(s)
| | | | | | | | - Thomas Boudier
- Sorbonne Universités, UPMC Univ Paris 06, 4 place Jussieu, 75005 Paris, France.
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31
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Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A. Fiji: an open-source platform for biological-image analysis. Nat Methods 2012. [PMID: 22743772 DOI: 10.1038/nmeth.2019.fiji] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.
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Affiliation(s)
- Johannes Schindelin
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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32
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Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A. Fiji: an open-source platform for biological-image analysis. Nat Methods 2012. [PMID: 22743772 DOI: 10.1038/nmeth.2019.pmid:22743772;pmcid:pmc3855844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.
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Affiliation(s)
- Johannes Schindelin
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A. Fiji: an open-source platform for biological-image analysis. Nat Methods 2012; 9:676-82. [PMID: 22743772 DOI: 10.1038/nmeth.2019] [Citation(s) in RCA: 33855] [Impact Index Per Article: 2821.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.
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Affiliation(s)
- Johannes Schindelin
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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Cardona A, Saalfeld S, Schindelin J, Arganda-Carreras I, Preibisch S, Longair M, Tomancak P, Hartenstein V, Douglas RJ. TrakEM2 software for neural circuit reconstruction. PLoS One 2012; 7:e38011. [PMID: 22723842 PMCID: PMC3378562 DOI: 10.1371/journal.pone.0038011] [Citation(s) in RCA: 586] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 04/28/2012] [Indexed: 11/24/2022] Open
Abstract
A key challenge in neuroscience is the expeditious reconstruction of neuronal circuits. For model systems such as Drosophila and C. elegans, the limiting step is no longer the acquisition of imagery but the extraction of the circuit from images. For this purpose, we designed a software application, TrakEM2, that addresses the systematic reconstruction of neuronal circuits from large electron microscopical and optical image volumes. We address the challenges of image volume composition from individual, deformed images; of the reconstruction of neuronal arbors and annotation of synapses with fast manual and semi-automatic methods; and the management of large collections of both images and annotations. The output is a neural circuit of 3d arbors and synapses, encoded in NeuroML and other formats, ready for analysis.
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Affiliation(s)
- Albert Cardona
- Institute of Neuroinformatics, University of Zurich and ETH Zurich, Zurich, Switzerland.
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Doube M, Kłosowski MM, Arganda-Carreras I, Cordelières FP, Dougherty RP, Jackson JS, Schmid B, Hutchinson JR, Shefelbine SJ. BoneJ: Free and extensible bone image analysis in ImageJ. Bone 2010; 47:1076-9. [PMID: 20817052 PMCID: PMC3193171 DOI: 10.1016/j.bone.2010.08.023] [Citation(s) in RCA: 1125] [Impact Index Per Article: 80.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 08/26/2010] [Accepted: 08/27/2010] [Indexed: 11/26/2022]
Abstract
Bone geometry is commonly measured on computed tomographic (CT) and X-ray microtomographic (μCT) images. We obtained hundreds of CT, μCT and synchrotron μCT images of bones from diverse species that needed to be analysed remote from scanning hardware, but found that available software solutions were expensive, inflexible or methodologically opaque. We implemented standard bone measurements in a novel ImageJ plugin, BoneJ, with which we analysed trabecular bone, whole bones and osteocyte lacunae. BoneJ is open source and free for anyone to download, use, modify and distribute.
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Affiliation(s)
- Michael Doube
- Department of Bioengineering, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom. ;
- Corresponding author: , Phone: +44 (0)20 7594 7426, Fax: +44 (0)20 7594 9817
| | - Michał M Kłosowski
- Department of Bioengineering, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom. ;
| | - Ignacio Arganda-Carreras
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139 USA. Phone: (001) 617-452-4976
| | - Fabrice P Cordelières
- Institut Curie, Section de Recherche, Plate-forme d’Imagerie Cellualire et Tissulaire, CNRS UMR 3348, Centre Universitaire, Bât. 112, Orsay 91405, France. Phone: +33 1 6986 3130
| | | | - Jonathan S Jackson
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02445, USA. Phone: (001) 617-732-6012
| | - Benjamin Schmid
- Department of Neurobiology and Genetics, University of Würzberg, Germany. Phone: +49 (0)931 8884466
| | - John R Hutchinson
- Structure and Motion Laboratory, The Royal Veterinary College, North Mymms, Hatfield, Hertfordshire AL9 7TA, United Kingdom.
| | - Sandra J Shefelbine
- Department of Bioengineering, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom. ;
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Arganda-Carreras I, Sorzano COS, Thévenaz P, Muñoz-Barrutia A, Kybic J, Marabini R, Carazo JM, Ortiz-de Solorzano C. Non-rigid consistent registration of 2D image sequences. Phys Med Biol 2010; 55:6215-42. [DOI: 10.1088/0031-9155/55/20/012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Arganda-Carreras I, Fernández-González R, Muñoz-Barrutia A, Ortiz-De-Solorzano C. 3D reconstruction of histological sections: Application to mammary gland tissue. Microsc Res Tech 2010; 73:1019-29. [DOI: 10.1002/jemt.20829] [Citation(s) in RCA: 423] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Sorzano COS, Arganda-Carreras I, Thévenaz P, Beloso A, Morales G, Valdés I, Pérez-García C, Castillo C, Garrido E, Unser M. Elastic image registration of 2-D gels for differential and repeatability studies. Proteomics 2008; 8:62-5. [DOI: 10.1002/pmic.200700473] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Arganda-Carreras I, Fernandez-Gonzalez R, Ortiz-de-Solorzano C. Automatic registration of serial mammary gland sections. Conf Proc IEEE Eng Med Biol Soc 2007; 2004:1691-4. [PMID: 17272029 DOI: 10.1109/iembs.2004.1403509] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We present two methods for automatic registration of microscope images of consecutive tissue sections. They represent two possibilities for the first step in the 3-D reconstruction of histological structures from serially sectioned tissue blocks. The goal is to accurately align the sections in order to place every relevant shape contained in each image in front of its corresponding shape in the following section before detecting the structures of interest and rendering them in 3D. This is accomplished by finding the best rigid body transformation (translation and rotation) of the image being registered by maximizing a matching function based on the image content correlation. The first method makes use of the entire image information, whereas the second one uses only the information located at specific sites, as determined by the segmentation of the most relevant tissue structures. To reduce computing time, we use a multiresolution pyramidal approach that reaches the best registration transformation in increasing resolution steps. In each step, a subsampled version of the images is used. Both methods rely on a binary image which is a thresholded version of the Sobel gradients of the image (first method) or a set of boundaries manually or automatically obtained that define important histological structures of the sections. Then distance-transform of the binary image is computed. A proximity function is then calculated between the distance image of the image being registered and that of the reference image. The transformation providing a maximum of the proximity function is then used as the starting point of the following step. This is iterated until the registration error lies below a minimum value.
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Arganda-Carreras I, Sorzano COS, Marabini R, Carazo JM, Ortiz-de-Solorzano C, Kybic J. Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization. Computer Vision Approaches to Medical Image Analysis 2006. [DOI: 10.1007/11889762_8] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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