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Image Processing

NeuronStudio provides a number of image processing routines (filters) that can be used to enhance visualization, or improve the quality of traced models and spine analysis.

Among the various filters provided are blurring, inversion, brightness/contrast, dynamic range, and more. See also the menu item Run >> Image Filter for a complete list of available filters.

IMPORTANT: Currently there is no interface for setting parameters to the image processing routines. You will need to edit and save the .ns configuration file to change the default parameters. Note that the name of the image filter is suffixed with a ... to indicate that, in future versions, a window containing interface elements for setting the various parameters will be implemented.

Example: (Running a Brightness/Contrast Filter)

1) Browse to the location of the executable. Open the .ns file in any standard text editor.

2) Search for the name of the image processing routine surrorunded by brackets. In this case [brightness_contrast].

3) Set the brightness and contrast to appropriate values, e.g. 0.0 for brightness and 0.45 for contrast.

4) Save the .ns file.

5) Select Run >> Image Filter >> Brightness/Contrast... from the menu.

Note that if the name of the filter is suffixed with an MP, it means that the filter has been optimized to use multiple processors (CPU's) if they are available. If your machine has more than one processor or is dual-core, quad-core, etc., then setting the number of CPU's will provide a speed enhancement when these filters are run, especially on large datasets. Select the menu item Run >> Number of CPU's to set this value. By allowing the user to set the number of CPU's instead of automatically detecting them, we allow for control of the amount of parallelism used.

IMPORTANT: The image processing filters cannot be undone. A progress window will appear for lengthy operations but pressing cancel will simply terminate the filter, not revert any processed data back to its state before the filter was run.

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