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Mouse Connectome Project edited this page May 3, 2019 · 20 revisions

Dashboard Page

Searching

Global Text Search

Global Search helps you to filter your table data based on different categories like Injection Site, Tracers, Case Ids. You can select any category from the dropdown and type in some text that matches the selected category with the help of auto complete drop down.
Select a brain region to see a list of cases in which a tracer injection has been made in that location, e.g., Anterior Cingulate Cortical Area (ACA). Search can be performed by the full name or the acronym of the brain region according to the Allen Reference Atlas.
or select tracer for region of interest,

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Viz Search

Anterograde tracers injected into a region of interest label the region's output projections. These tracers label axons and their terminal branches. Choose anterograde if you would like to view cases with anterograde tracers in your region of interest that show its output projections.

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Retrograde tracers injected into a region of interest label all brain structures that provide input to the region. These tracers label the cell bodies of projection neurons that send inputs to the region of interest. Choose retrograde if you would like to view cases with retrograde tracers in your region of interest that show its input connections.

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Filters

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Project (# of cases)

Select the name of a project to get a list of its associated cases. For example, choosing Hippocampus will return all tracer injection cases that were used to assess the connectivity architecture of the hippocampus.

Gene expression

For select brain regions, in addition to connectivity information, gene expression data also is available through our collaborations with UCSD. The areas for which gene expression data is also available are indicated with the "insert symbol" symbol. Gene expression data for the region can be attained by clicking on "insert symbol".

Metrics filters

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  • iConnectome: Total number of cases which are available to view in iConnectome Cell Type Viewer.
  • Map: Total number of cases which are available to view in iConnectome Cell Type Map Viewer.
  • Gene: Total number of cases which are available to view the gene expression data of the injection sites regions on UCSD web portal.

Table

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Columns

  • Case ID
  • Injection Site, Tracer, and ARA levels
  • Projects and navigation buttons
  • Image gallery

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Navigating to viewers

  • iConnectome Cell Type Viewer

When the users want to view a specific case on the iConnectome Viewer, click on the "case id" bubble will open up a new window to view the case of your interest.

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  • iConnectome Cell Type Map Viewer

Navigation to the iConnectome Cell Type Map Viewer has two different options to view the labelings.

First, similar to the iConnectome Cell Type Viewer navigation, the users can chose a specific interest of a case by clicking "case id" bubble. The bubble will open up a new window to view the case of your interest.

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Second, the users can pick the labels of the tracers of interested case(s). Selected cases will appear on the cart when the hamburger is clicked. After the users verifies the combination of labelings to view, click on the view button will open a viewer window.

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Metrics

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  • Total cases: Total number of cases available on the Mouse Connectome Project data repository.

  • Injection sites: Total number of injection sites.

  • Pathways: Total number of projection pathways.

  • iConnectome: Total number of cases which are available to view in iConnectome Cell Type Viewer.

  • Map: Total number of cases which are available to view in iConnectome Cell Type Map Viewer.

  • Gene: Total number of cases which are available to view the gene expression data of the injection sites regions on UCSD web portal.

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