Scientific Visualization

Scientific Visualization

  • Faezeh Iranmanesh added an answer:
    How to export a file in Microvisu3D format from Amira?

    Hi everybody

    I want to save an image which constructed in Amira software in Microvisu3d format (.mv3d).Does anyone know if it is possible to save an image in this format? I only know Amira can open a file in this format but I don't know how I can save a file in this format.

    Faezeh Iranmanesh

    Thanks a lot!

  • Harnois Maxime added an answer:
    Experience with using visuals to communicate your research.
    If you are willing to publicly share your experiences, I am very interested to hear your thoughts on the use of visual communication for scientific research. Specifically, I am interested in learning:
    - your thoughts on the importance of visuals
    - the type of software you use to create charts, graphs, schematics, illustrations
    - how much time you spend creating these visuals
    - your thoughts on the value of outside expertise to help you create your visuals
    Harnois Maxime

    Inkscape for 2D and Blender for 3D pictures.

    Blender for animations
    For instance:

  • Paulo Carvalho added an answer:
    What are the methods of information visualization?

    Whether there is classical textbooks, lectures on methods of data visualization

    Paulo Carvalho

    In deed, it seems to be a very interesting course.

    Thank you Christos.

  • Harnois Maxime added an answer:
    Can anyone suggest an open source software to make scientific diagrams?

    I am always fascinated by the kind of diagrams that people publish in Cell, Nature, Science etc.. I want to get such a software that can help me in my research.

    Harnois Maxime

    Inkscape for 2D and Blender for 3D pictures.

    Blender for animations
    For instance:

  • Jochen Wilhelm added an answer:
    How to elegantly show multiple significant differences between groups on a bar graph?
    I have measured gene expression across eight time points, and multiple comparisons show many differences between the time points. I'd like to indicate these significant differences on my bar graph. Usually I would draw a line above the relevant bars and put * or ** above the line, but there are so many differences that the lines would become unwieldy and I feel my graph would just look too messy! Any suggestions? Should I just relegate the p values to a table?
    Jochen Wilhelm

    I see. So you can possibly take initials or abbreviations of these interventions, like

    D Significant difference from Dolomitrin-treatment
    M Significant difference from Melomycin-treatment
    Pa Significant difference from Palatosan-treatment
    Pi Significant difference from Parsitin-treatment

    and so on.

  • Manish Kashyap added an answer:
    Any good experiences with Matlab alternatives?
    I am evaluating various Open Source tools for use in EE resarch. Few interesting ones would be Octave, SciLab, Python with Numpy and SciPy. Anyone care to share experiences, good or bad? Any other suggestions?
    Manish Kashyap

    GNU Octave is very useful as it provides the best alternative to MATLAB in terms of MATLAB compatibility. There ate huge amount of common toolboxes in both with similar function syntax. Octave 4.0.0 is released with GUI interface which is very much similar to MATLAB. Here you can find some video tutorials on OCTAVE 4.0.0 for image processing together with step by step installation.

  • Bernard André Alain Chabot added an answer:
    How can I download your visualization ontology?
    I've tried to upload your visualization ontology : in Protégé 3.5, but I encountered a error. Did you check such a import?
    • Source
      [Show abstract] [Hide abstract]
      ABSTRACT: Research papers are published in various digital libraries, which deploy their own meta-models and technologies to manage, query, and analyze scientific facts therein. Commonly they only consider the meta-data provided with each article, but not the contents. Hence, reaching into the contents of publications is inherently a tedious task. On top of that, scientific data within publications are hardcoded in a fixed format (e.g. tables). So, even if one manages to get a glimpse of the data published in digital libraries, it is close to impossible to carry out any analysis on them other than what was intended by the authors. More effective querying and analysis methods are required to better understand scientific facts. In this paper, we present the web-based CODE Visualisation Wizard, which provides visual analysis of scientific facts with emphasis on automating the visualisation process, and present an experiment of its application. We also present the entire analytical process and the corresponding tool chain, including components for extraction of scientific data from publications, an easy to use user interface for querying RDF knowledge bases, and a tool for semantic annotation of scientific data sets.
      Full-text · Conference Paper · Jan 2014
    Bernard André Alain Chabot
    OK. It works fine. Thks !
  • Giovanni Pintore added an answer:
    What's a good visualization tool for a presentation?
    I am searching for a good visualization tool for presenting my research results in a conference. Do you have any fancy tools in mind?
    Giovanni Pintore
    I suggest Powerpoint too
  • Nancy Rodriguez added an answer:
    Which free software would you recommend for high quality 3D scientific visualisation?
    I use Paraview and have experimented with Mayavi for 3D visualisation (volume rendering, surface plots etc.). I find Paraview can be lacking in quality at times and Mayavi has been difficult to use - are there any alternatives people could recommend?
    Nancy Rodriguez
    VTK is also a widely know software for visualization


  • Roy Trevor Williams added an answer:
    How important is storytelling and visualization for your science?
    Two weeks ago, I attended two interesting presentations, one of a British SME (shoothill) on visualizing scientific data for the public (for example applying a technique known as Deep Zoom), the other of the Polytechnic University of Milan on using NASA world wind as a virtual globe in the area of environmental modeling. Both make me think of the role of visualizing research results depending on the target audience and about telling the right story to the right people. I have the feeling that in my filed (geospatial information science and Digital Earth), we still miss a strong commitment to such ideas and also education has to increase on related topics. Do you share this view / maybe also in other research areas? What are your experiences?
    Roy Trevor Williams
    Hi, visualisation is essential to what we are doing, which is to try to describe the dynamics of learning in open (emergent) systems. We have developed a 3D footprint that tracks 25 variables, simultaneously, across a learning event. It could still do with some automation and interactivity, but its working for us (and for others, too).

  • Irene Baron added an answer:
    What is the future of scientific illustration?
    Hi there,

    I'd love to hear your thoughts about what you think will be the next generation scientific visualization approach. Will it be interactive? More photo-realistic? What are the skills we need to learn today to keep up in the future?

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