Mesoscale microscopy and image analysis tools for understanding the brain

被引：24
|
作者：
Tyson, Adam L. [1 ]
Margrie, Troy W. [1 ]
机构：
[1] UCL, Sainsbury Wellcome Ctr, 25 Howland St, London W1T 4JG, England
来源：
PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY | 2022年 / 168卷
基金：
英国惠康基金;
关键词：
Neuroscience; whole Brain microscopy; Image registration; Segmentation; Visualisation; GENE-EXPRESSION; 3-DIMENSIONAL VISUALIZATION; AXONAL PROJECTIONS; RESOLUTION; FRAMEWORK; ATLAS; RECONSTRUCTION; CONNECTIVITY; TOMOGRAPHY; ANNOTATION;
D O I：
10.1016/j.pbiomolbio.2021.06.013
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
Over the last ten years, developments in whole-brain microscopy now allow for high-resolution imaging of intact brains of small animals such as mice. These complex images contain a wealth of information, but many neuroscience laboratories do not have all of the computational knowledge and tools needed to process these data. We review recent open source tools for registration of images to atlases, and the segmentation, visualisation and analysis of brain regions and labelled structures such as neurons. Since the field lacks fully integrated analysis pipelines for all types of whole-brain microscopy analysis, we propose a pathway for tool developers to work together to meet this challenge.
引用
收藏
页码：81 / 93
页数：13
相关论文
共 50 条
  • [31] Physics-based reward driven image analysis in microscopy
    Barakati, K.
    Yuan, Hui
    Goyal, Amit
    Kalinin, S. V.
    DIGITAL DISCOVERY, 2024, 3 (10): : 2061 - 2069
  • [32] Quantitative neuroanatomy of all Purkinje cells with light sheet microscopy and high-throughput image analysis
    Silvestri, Ludovico
    Paciscopi, Marco
    Soda, Paolo
    Biamonte, Filippo
    Iannello, Giulio
    Frasconi, Paolo
    Pavone, Francesco S.
    FRONTIERS IN NEUROANATOMY, 2015, 9
  • [33] Between neurons and networks: investigating mesoscale brain connectivity in neurological and psychiatric disorders
    Silveira, Ana Clara Caznok
    Antunes, Andre Saraiva Leao Marcelo
    Athie, Maria Carolina Pedro
    da Silva, Barbara Filomena
    dos Santos, Joao Victor Ribeiro
    Canateli, Camila
    Fontoura, Marina Alves
    Pinto, Allan
    Pimentel-Silva, Luciana Ramalho
    Avansini, Simoni Helena
    de Carvalho, Murilo
    FRONTIERS IN NEUROSCIENCE, 2024, 18
  • [34] Cell Membrane Tracking in Living Brain Tissue Using Differential Interference Contrast Microscopy
    Lee, John
    Kolb, Ilya
    Forest, Craig R.
    Rozell, Christopher J.
    IEEE TRANSACTIONS ON IMAGE PROCESSING, 2018, 27 (04) : 1847 - 1861
  • [35] A Baboon Brain Atlas for Magnetic Resonance Imaging and Positron Emission Tomography Image Analysis
    Agaronyan, Artur
    Syed, Raeyan
    Kim, Ryan
    Hsu, Chao-Hsiung
    Love, Scott A.
    Hooker, Jacob M.
    Reid, Alicia E.
    Wang, Paul C.
    Ishibashi, Nobuyuki
    Kang, Yeona
    Tu, Tsang-Wei
    FRONTIERS IN NEUROANATOMY, 2022, 15
  • [36] Understanding metric-related pitfalls in image analysis validation
    Reinke, Annika
    Tizabi, Minu D.
    Baumgartner, Michael
    Eisenmann, Matthias
    Heckmann-Noetzel, Doreen
    Kavur, A. Emre
    Raedsch, Tim
    Sudre, Carole H.
    Acion, Laura
    Antonelli, Michela
    Arbel, Tal
    Bakas, Spyridon
    Benis, Arriel
    Buettner, Florian
    Cardoso, M. Jorge
    Cheplygina, Veronika
    Chen, Jianxu
    Christodoulou, Evangelia
    Cimini, Beth A.
    Farahani, Keyvan
    Ferrer, Luciana
    Galdran, Adrian
    van Ginneken, Bram
    Glocker, Ben
    Godau, Patrick
    Hashimoto, Daniel A.
    Hoffman, Michael M.
    Huisman, Merel
    Isensee, Fabian
    Jannin, Pierre
    Kahn, Charles E.
    Kainmueller, Dagmar
    Kainz, Bernhard
    Karargyris, Alexandros
    Kleesiek, Jens
    Kofler, Florian
    Kooi, Thijs
    Kopp-Schneider, Annette
    Kozubek, Michal
    Kreshuk, Anna
    Kurc, Tahsin
    Landman, Bennett A.
    Litjens, Geert
    Madani, Amin
    Maier-Hein, Klaus
    Martel, Anne L.
    Meijering, Erik
    Menze, Bjoern
    Moons, Karel G. M.
    Mueller, Henning
    NATURE METHODS, 2024, 21 (02) : 182 - 194
  • [37] Review of free software tools for image analysis of fluorescence cell micrographs
    Wiesmann, V.
    Franz, D.
    Held, C.
    Muenzenmayer, C.
    Palmisano, R.
    Wittenberg, T.
    JOURNAL OF MICROSCOPY, 2015, 257 (01) : 39 - 53
  • [38] Automatic brain MR image segmentation by relative thresholding and morphological image analysis
    Li, Kai
    Malony, Allen D.
    Tucker, Don M.
    VISAPP 2006: PROCEEDINGS OF THE FIRST INTERNATIONAL CONFERENCE ON COMPUTER VISION THEORY AND APPLICATIONS, VOL 1, 2006, : 354 - +
  • [39] Robust image alignment for cryogenic transmission electron microscopy
    McLeod, Robert A.
    Kowal, Julia
    Ringler, Philippe
    Stahlberg, Henning
    JOURNAL OF STRUCTURAL BIOLOGY, 2017, 197 (03) : 279 - 293
  • [40] Brain Tumor Detection Using MRI Image Analysis
    Bhattacharyya, Debnath
    Kim, Tai-hoon
    UBIQUITOUS COMPUTING AND MULTIMEDIA APPLICATIONS, PT II, 2011, 151 : 307 - +
12345