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Region of Interest (ROI)

NeuronStudio allows you to define a region of interest having a 3-dimensional rectangular shape. It has a dual purpose of limiting certain operations to its boundaries, as well as for visualizing subsets of the data.

For Visualization

Select the ROI Tool tool from the tools panel or use the menu item Edit >> Mode >> R.O.I. to begin defining an R.O.I. Move the mouse over the corners of the R.O.I. and click and drag to resize the dimensions. Click and drag anywhere within the interior of the rectangle to translate the region. This can be done of course in any of the three views in the 2-dimensional display.

Defining an ROI

Note that the R.O.I. being defined here does not take effect for visualization yet. Select the menu item Run >> Visualize R.O.I. or hit the F9 key to visualize the current region.

IMPORTANT: The projections and volume renderings are automatically regenerated when the R.O.I. is visualized.

Visualizing an ROI

The data that is not contained within the R.O.I. is drawn by default in a grey color (in the 2D display). Using this technique you can acheive order of magnitudes speedup in the projection and volume rendering of large datasets. Note also that there is no limit to the number of times you may define and/or visualize a region.

If you choose to save the dataset or projections, the resulting images will be the same size as the visualized R.O.I.

For Operations

In addition to the visualization function of the R.O.I. a number of program features are constrained to its boundaries. Some of these include: spine analysis, automated tracing, adding measurements, adding manual spines, and image processing.

Note that there is no second step required to make the R.O.I. functional in terms of limiting the above operations, as was required for visualization. In other words simply setting the shape of the region using the ROI Tool tool is enough.

IMPORTANT: The current shape of the R.O.I. is used to bound the operations. The size of the R.O.I. when (and if) sub-sections of the dataset were visualized is not used.

In the image below, an R.O.I. has been defined. Note that the boundaries of this R.O.I. have been changed since the last time an R.O.I. was visualized (dark grey region indicates the data that is not being visualized). If for example, manual spine addition was the operation that you want to perform, you must click within the R.O.I. in order to be able to add a spine.

Using an R.O.I. for limiting operations.

3D Manipulation

You may also manipulate the dimensions of the R.O.I. from within the 3D window. Click and drag on any one of the controls (grey arrows) to move the position of the corresponding face. As in 2D, the R.O.I. dimensions are bounded by the dimensions of the image volume. The image below shows the selection of the arrow control in 3D for the near face.

Resizing the R.O.I. in 3D.

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Send questions or comments to: alfredo.rodriguez@mssm.edu