Biological imaging software tools

Eliceiri, Kevin W.; Berthold, Michael R.; Goldberg, Ilya G.; Ibáñez, Luis; Manjunath, B.S.; Martone, Maryann E.; Murphy, Robert F.; Peng, Hanchuan; Plant, Anne L.; Roysam, Badrinath; Stuurman, Nico; Swedlow, Jason R.; Tomančák, Pavel; Carpenter, Anne E.

doi:10.1038/nmeth.2084

Cited by 488 publications

(408 citation statements)

References 61 publications

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“…7,8 A spectacular enhancement in the quantitative power of microscopy techniques is currently being driven by technological advances, which include the development of (1) protocols that render organs almost completely transparent for volumetric imaging 9 ; (2) novel modalities of optical imaging such as light sheet microscopy or optical projection tomography for faster, automated acquisition of multidimensional images of large tissue regions or entire organs 10,11 ; (3) more sophisticated excitation and detection systems that enable increased multiplexing; and (4) bioimage-based analysis software tools to facilitate the unbiased extraction of cytometric measurements and computation of quantitative spatial information from complex, high-dimensional data sets. 12 Thus, it is now becoming possible to generate and analyze organ-wide three-dimensional (3D) reconstructions of a variety of tissues including BM and spleen with cellular and subcellular resolution (Figure 1). [13][14][15] Collectively, multidimensional microscopy techniques hold great promise to take our understanding of the global microanatomy of hematopoiesis to the next level, that is, one in which distinct stages of development along the hematopoietic continuum are precisely resolved and mapped into a panoramic view of BM topology.…”

Section: Methodological Approaches and Advances To Study Bm Tissuesmentioning

confidence: 99%

Quantification and three-dimensional microanatomical organization of the bone marrow

2017

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Bone marrow (BM) constitutes one of the largest organs in mice and humans, continuously generating, in a highly regulated manner, red blood cells, platelets, and white blood cells that together form the majority of cells of the body. In this review, we provide a quantitative overview of BM cellular composition, we summarize emerging knowledge on its structural organization and cellular niches, and we argue for the need of multidimensional approaches such as recently developed imaging techniques to uncover the complex spatial logic that underlies BM function in health and disease.Since Neumann and Bizzozero independently proposed in 1868 that the origin of blood cells was to be found in soft tissues contained inside bone cavities, the bone marrow (BM) has continued to fascinate scientists and clinicians alike. 1,2 Yet more than a century later, our understanding of how the hematopoietic, immune, and bone-forming tasks of the BM are tightly controlled and integrated in the context of one common anatomical space is still incomplete. Methodological approaches and advances to study BM tissuesEarly studies on BM cellular composition and microarchitecture date back to the 19th century when the first biopsies of marrow content were performed in living individuals. 3 Microscopic observation of BM smears and examination of histological sections became the standard technique, which is still used to this day to study, diagnose, and classify hematologic disorders. The realization in the post-World War II era that transplantation of BM cells from healthy individuals could rescue the lethal effects of high-dose irradiation on hematopoiesis galvanized scientific interest in BM and lead to the development of methods to detect and measure hematopoietic stem and progenitor cell (HSPC) activity, absolute cellularity, lineage-specific half-lives, and kinetics of cell production in the BM of humans and in laboratory animals. 4,5 Gradual improvements in light and electron microscopy further refined the understanding of the quantitative composition and ultrastructural features of BM tissues. 6 The biggest leap in the fields of immunology and hematology came with the advent of recombinant antibody technology and flow cytometry in the 1960s. These breakthroughs permitted the identification, quantification, and isolation of diverse populations from highly heterogeneous cell suspensions through detection of phenotypic traits. 5 Indeed, to this day, flow cytometry remains the technological mainstay for the study and dissection of the hematopoietic system.Immunolabeling methods were further adopted in modern fluorescence-based microscopy to discriminate cellular phenotypes in tissue sections and study cellular organization in the BM. In recent years, confocal microscopy has become the most popular modality to define spatial relationships and study developmental-stage specific localization patterns, with a keen interest of many groups in the dissection of HSPC niches. 7 In addition, intravital multiphoton microscopy is employed to obtain dyna...

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Section: Methodological Approaches and Advances To Study Bm Tissuesmentioning

confidence: 99%

Quantification and three-dimensional microanatomical organization of the bone marrow

2017

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“…In fact, a shift of this weighting towards bioimage informatics within quantitative biology is to be expected more and more in the future. In this context, both the computational instrumentation and, moreover, the ability to apply image and data analysis will define the future perspectives of scientists in the life sciences (Carpenter et al, 2012; Eliceiri et al, 2012; Myers, 2012). …”

Section: Data Analysis and Data Managementmentioning

confidence: 99%

Advanced light microscopy core facilities: Balancing service, science and career

Ferrando‐May

Hartmann

Reymann

et al. 2016

Microsc. Res. Tech.

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Core Facilities (CF) for advanced light microscopy (ALM) have become indispensable support units for research in the life sciences. Their organizational structure and technical characteristics are quite diverse, although the tasks they pursue and the services they offer are similar. Therefore, throughout Europe, scientists from ALM‐CFs are forming networks to promote interactions and discuss best practice models. Here, we present recommendations for ALM‐CF operations elaborated by the workgroups of the German network of ALM‐CFs, German Bio‐Imaging (GerBI). We address technical aspects of CF planning and instrument maintainance, give advice on the organization and management of an ALM‐CF, propose a scheme for the training of CF users, and provide an overview of current resources for image processing and analysis. Further, we elaborate on the new challenges and opportunities for professional development and careers created by CFs. While some information specifically refers to the German academic system, most of the content of this article is of general interest for CFs in the life sciences. Microsc. Res. Tech. 79:463–479, 2016. © 2016 THE AUTHORS MICROSCOPY RESEARCH AND TECHNIQUE PUBLISHED BY WILEY PERIODICALS, INC.

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“…Image analysis in biology has become popular more recently compared with other scientific fields, such as astronomical physics and geology. We briefly review the conventional biomedical image processing systems and screen-updating techniques related to our system, see [18,20] and references therein for excellent surveys on general biomedical image processing tools.…”

Section: Related Workmentioning

confidence: 99%

“…The development of image-processing tools has become popular in biological and medical applications; in addition, rapid advances are being made in biomedical imaging technology [20,57,19]. In particular, tools that can manage large amounts of volumetric data (i.e., three-dimensional (3D) images) are required in advanced applications such as surgery simulations based on Computed Tomography (CT) volumes and quantitative analysis of live-cell images in molecular cell biology.…”

Section: Introductionmentioning

confidence: 99%

Communication Platform for Image Analysis and Sharing in Biology

Murakami

Tawara

Nishimura

et al. 2014

IJNC

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Image analysis is crucial to medical and biological applications. Recent advances in imaging technology have led to the demand for processing and visualizing a large amount of three-dimensional (3D) biomedical images. In addition, cloud computing has become popular for managing big data. Unfortunately, conventional image-processing systems either lack cloud computing services or advanced 3D processing abilities. In this paper, we present a novel cloud-based system for sharing, processing, and visualizing 3D biomedical images. Our system employs a standard web browser as a client interface that interactively communicates with high-performance servers. Thus, an inexpensive tablet PC without an advanced graphics processing unit (GPU) can be used for 3D image processing and visualization. Our system provides the sharing of limited software and hardware resources, and it allows for effective collaboration between researchers. We demonstrate the applicability and functionality of the system by examining typical case studies on biomedical images. We also examine the performance of our system numerically.

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Biological imaging software tools

Cited by 488 publications

References 61 publications

Quantification and three-dimensional microanatomical organization of the bone marrow

Quantification and three-dimensional microanatomical organization of the bone marrow

Advanced light microscopy core facilities: Balancing service, science and career

Communication Platform for Image Analysis and Sharing in Biology

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