Table of Contents

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Neuroterrain Atlas Client plugin

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User Manual

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Introduction

The Neuroterrain Atlas Client plugin is a viewer for data sets hosted on Neuroterrain Atlas Servers. These data sets are continuous three dimensional sets which can be viewed at any arbitrary plane, may have attached segmentation (labels) and alternate image channels (eg. fluorescence). Multiple sessions (including MBL viewer sessions) may be linked for co-navigation.

Starting the client

To select a data set for viewing

1. Open the Viewer Workspace.
2. In the Layer Controls, open the dropdown menu to the right of the Add Layer button.
3. Select Neuroterrain atlas client.
4. Select the server address of the Neuroterrain server hosting the data set you wish to use, or type it into the box.
   • If you are typing an address, enter the server's port number (obtained from the group hosting the server) into the port text box
   • The server address and port will be saved for future use.
5. Click on the Login button.
6. If more than one data set is hosted on the server, select the set you wish to see from the list of data sets presented.

To show labels/alternate image channels

• Select the label you wish to work with from the combo box in the Channels and Labels section.
• Change the visibility of the label using the _Vis check box.
• Change the saturation or intensity of the label using the Dim check box.
• Change the color of the label using the Color button.
• Turn label or channel display on or off using the show/hide button at the right selection box

To change the slicing axis

• Select the desired axis from the radio buttons in the Slicing Axis section.

To change the virtual knife position and angle

• The offset slider/spinner controls the knife position along the slicing axis
• The X, Y, and Z rotation slider/spinners control rotation of the virtual knife about the three main axes.

Linking sessions

1. Open two or more sessions (you may link either MBL or Neuroterrain sessions)
2. Select the session which you want to link from the "Link to" combo box. (Already linked sessions are in italic face, and unlinked sessions are in plain face.)
3. Unlink one session by selecting it again from the "Link to" box, or unlink all sessions by selecting "Unlink all".

User Interface

• Show/Hide: button to show/hide the layer in the viewport
• Expand/Collapse: button to expand/collapse the UI controls

• Expand/Collapse (Server and Session): button to expand/collapse the server/session controls
  • Server selection: combo box to select/specify the Neuroterrain server to use
  • port: text entry for the Neuroterrain server communication port
  • Login/Logout: button to log in to or out of the Neuroterrain server
  • link to: combo box to select other Neuroterrain or MBL sessions to co-navigate
• Expand/Collapse (Channels and Labels): button to expand/collapse the channel/label controls
  • Channel selection: combo box to select channels for display/modification
  • Channel show/hide: button to toggle visibility of alternate image channels
  • Channel visibility: checkbox to set display state of selected channel
  • Channel color: button to set display color of selected channel
  • Label selection: combo box to select labels for display/modification
  • Label show/hide: button to toggle visibility of labels
  • Label visibility: checkbox to set display state of selected label
  • Label dim: checkbox to set the bright/dim state of selected label
  • Label color: button to set display color of selected label
• Expand/Collapse (Slicing Axis): button to expand/collapse the slicing axis controls
  • Coronal: radio button to select coronal (z) slicing axis
  • Sagittal: radio button to select sagittal (x) slicing axis
  • Horizontal: radio button to select horizontal (y) slicing axis
• Expand/Collapse (Knife Position): button to expand/collapse the knife positioning controls
  • offset: slider/spinner to move virtual knife along slicing axis
  • X rotation: slider/spinner to rotate virtual knife around the X axis
  • Y rotation: slider/spinner to rotate virtual knife around the Y axis
  • Z rotation: slider/spinner to rotate virtual knife around the Z axis

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Functional Specification

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Data input methods

Add layer only

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Serializing/deserializing

In the serialization process, following states are saved:

• Server selection
• Channel and label state
• Slicing axis
• Virtual knife position/orientation
• Linking/co-navigation states are not saved

• Rotation
• Scaling
• Translation
• Brightness
• Contrast
• Opacity
• X-Flip, Y-Flip, Z-Filp values

The deserialization process restores all the above saved states.

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Linking

• Neuroterrain-Neuroterrain: Changes in the virtual knife position/orientation are reflected in all linked sessions. This includes changes in slicing axis. Changes in channel/label visibility do not affect linked sessions.
• Neuroterrain-MBL: Changes in virtual knife position/orientation result in the MBL section closes to the current virtual knife position being displayed. Changing MBL section results in the equivalent plane in the Neuroterrain session being displayed. (Note that this equivalent plane is only valid for the Neuroterrain atlas the MBL set was registered to, but there is no constraint on what Neuroterrain session is linked to.)

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Workspace Interoperability

None.

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Error Handling

All errors are handled internally, with user notification where appropriate. No exceptions thrown.

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CarlGustafson - 28 Apr 2009