A virtual lab-notebook for multidimensional microscope images

Boon, Paul; Eminovic, N.; Vos, A. de; Buitendijk, Bram; Raaij, E. J. van; Broeder, Marjo J. den; Hage, W.J.; Verbeck, F.J.

doi:10.1109/iv.2000.859754

Cited by 3 publications

(4 citation statements)

References 4 publications

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“…The contours are obtained from the TDR-3Dbase software package 3,7,13,14,15,17 . This software platform is normally used to produce an initial and comprehensive 3D reconstruction from plan parallel images 14,15,17,18 .…”

Section: Contour Collectionmentioning

confidence: 99%

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<title>Data submission of 3D image sets to a bio-molecular database using active shape models and a 3D reference model for projection</title>

et al. 2003

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This paper discusses the application of the Active Shape Model as a tool to compute the orientation of a specimen that has been subjected to CLSM imaging. The images have captured patterns of gene expression and these will have to be submitted to and stored in a database. Having all of these patterns available will enable spatio-temporal mining of image data and other linked data. The applications discussed in this paper focus on the zebrafish model system. The gene expression database employs a 3D digital atlas as a reference system in combination with an Active Shape Model. The Active Shape Model is applied with a few anatomical structures and will be scaled up to be usable with more structures in the future.

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Section: Contour Collectionmentioning

confidence: 99%

“…All the data from the contour extraction are stored in a XML database 7,19 . Per image such database is constructed.…”

Section: Databasesmentioning

confidence: 99%

<title>Data submission of 3D image sets to a bio-molecular database using active shape models and a 3D reference model for projection</title>

et al. 2003

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“…The native format of our data is XML 11 . The data come from two sources, the first being our image acquisition station and the second being the software for annotation (TDR 3Dbase).…”

Section: The Use Of Xmlmentioning

confidence: 99%

<title>Visualization of complex data sets over Internet: 2D and 3D visualization of the 3D digital atlas of zebrafish development</title>

Verbeek

Boon

Sloetjes

et al. 2001

Internet Imaging III

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We have designed and implemented a 3D digital atlas of zebrafish development. In this paper we focus on the presentation of the data of this atlas using the Internet. An important part of the data of this atlas is graphical. Therefore special effort is put into fast and comprehensive visualization of the 2D and 3D graphical data, i.e. images and their annotations as well as the 3D models that arise from the application of the annotation process on a coherent 3D dataset. These data are presented to the end-user and the modes of visualization need be linked to provide the user with feedback. The success of visualization over the Internet is partially depending on the transfer time of the data as well as the computational load of the data at the client side. The applications discussed in this paper are optimized for transfer time and computational load.

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“…Offering standardized ways of storing data and providing ad-hoc mechanisms to categorize information in realtime, they have set scientists free to focus on more important tasks. Gradually, ELNs have shifted themselves from complementary tools to indispensable lab mechanisms in many areas of research such as biology, medicine, materials science, bioinformatics, geoscience, and astronomy [9]- [11].…”

Section: Introductionmentioning

confidence: 99%

Solar Lab Notebook (SLN): An Ultra-Portable Web-Based System for Heliophysics and High-Security Labs

Tsalaportas¹,

Kapinas²,

Karagiannidis³

2015

IEEE J. Sel. Top. Appl. Earth Observations Remote Sensing

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Abstract-This paper introduces the Solar Lab Notebook (SLN), an electronic lab notebook for improving the process of recording and sharing solar related digital information in an organized manner. SLN is a pure web-based application (available online: http://umbra.nascom.nasa.gov/sln) that runs client-side only, employing a clean and very friendly graphical user interface design, and thus providing a true cross-platform user experience. Furthermore, SLN leverages unique technologies offered by modern web browsers, such as the FileReader API, the Blob interface and Local Storage mechanism; it is coded entirely using HTML5, CSS3, and JavaScript, and powered by the extremely well documented XML file format. For highsecurity labs, it can be utilized as an ultra-portable and secure digital notebook solution, since it is functionally self-contained, and does not require any server-side process running on either the local or a remote system. Finally, the W3C XML Schema language is used to define a list of rules, namely a data standard, that an SLN file must conform to in order to be valid. In this way, developers are able to implement their own validation functions in their projects, or use one of the freely available tools to check if a data file is properly structured. Similarly, scientific groups at different labs can easily share information, being confident about the integrity of the exchanged data.

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A virtual lab-notebook for multidimensional microscope images

Cited by 3 publications

References 4 publications

<title>Data submission of 3D image sets to a bio-molecular database using active shape models and a 3D reference model for projection</title>

<title>Data submission of 3D image sets to a bio-molecular database using active shape models and a 3D reference model for projection</title>

<title>Visualization of complex data sets over Internet: 2D and 3D visualization of the 3D digital atlas of zebrafish development</title>

Solar Lab Notebook (SLN): An Ultra-Portable Web-Based System for Heliophysics and High-Security Labs

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