Tools

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There are a variety of related projects and tools that we have incorporated to help your exploration.

Contents

[edit] Search Function


Use the search box to search for data of interest that exists in the Whole Brain Catalog. This search function takes advantage of the semantic capabilities provided by the Neuroscience Information Framework and NeuroLex and the Mulgara RDF triple store.

Double-clicking on a search result allows you to zoom to that object.


[edit] Probe Tool


The probe tool can be used to launch spatial queries, including finding gene expression data from the Allen Brain Atlas. Bring up the Probe from the View menu. Once the probe is in your desired location, right-click on the probe and navigate through the context menu as shown to the left. This will bring up a page in your web browser with the appropriate gene expression data.

Find more about conducting spatial queries here.

The probe tool is also helpful in navigation.



[edit] High resolution images in a web browser

To view high resolution images in your web browser, right-click on an image to bring up the context menu and select View in Web Browser.

We have integrated the ability to view images that are gigabytes. In order to explore multiple, massive datasets on your personal computer in a single environment we have implemented a design in which images are broken into tiles. Inspect the highest resolution view via your web browser through links from the Whole Brain Catalog.

We use MapServer and OpenLayers, the same technologies used in many geospatial projects including Google Maps and Google Earth, to display images that are from tens of megabytes to gigabytes in size.



[edit] Screenshots

Under the File menu you can select the Take Screenshot and an image of the entire window will be saved to a location specified by a pop up window.


[edit] Annotation Tool

Create an annotation about an object by right-clicking on the object to bring up the context menu and select Write Note About


[edit] Download Cell Models

Right clicking on a cell model will bring up a context menu that will let you select an option to download it as XML.


[edit] Mini-maps


The mini-maps allow you to orient yourself in the environment and see where you are located in the 3 dimensions of the brain. You can bring up the mini-maps under the View menu.

This takes advantage of render to texture features in the JMonkeyEngine.


[edit] NeuroLex

The NeuroLex project, supported by the Neuroscience Information Framework project, is a dynamic lexicon of neuroscience concepts that takes advantage of semantic mediawiki technology.

The NeuroLex is being constructed to help improve the way that neuroscientists communicate about their object data, so that information systems like the NIF can find data more easily and provide more powerful means of integrating data that occur across distributed resources. One of the big roadblocks to data integration in neuroscience is the inconsistent use of terminology in databases and other resources like literature. When we use the same terms to mean different things, we cannot easily ask questions that span across multiple resources.

The initial entries in the NeuroLex were built from the NIFSTD ontologies to get the project rolling. For more about the principles behind the NeuroLex, see How to Contribute to the NeuroLex.



Within the Whole Brain Catalog you can view any object's semantic information. Do this by right-clicking on the object in the environment or in the data list in the left panel to bring up the context menu. In the context menu, select Open in NeuroLex.org to bring up the NeuroLex page in your web browser.


[edit] Cell Centered Database

The goal of the CCDB project is to make unique and valuable datasets available to the scientific community for visualization, reuse and reanalysis. Data in the CCDB can be accessed by performing a Search or by browsing through their Gallery. Data in the CCDB may be downloaded freely and reused for non-profit use within the terms of their usage agreement.

The Whole Brain Catalog uses the CCDB as a data host. All data within the CCDB can be viewed within the environment.


[edit] Neuroscience Information Framework

The Neuroscience Information Framework (NIF; http://nif.nih.gov) is a dynamic inventory of Web-based neuroscience resources, data, and tools accessible via any computer connected to the Internet. An initiative of the NIH Blueprint for Neuroscience Research, NIF advances neuroscience research by enabling discovery and access to public research data and tools worldwide through an open source, networked environment.


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