### Tool: Map Filter

Map Filter includes several choices for smoothing or transforming volume data such as density maps. These capabilities are also available as various volume operation commands. See also: Volume Viewer, Hide Dust, Segment Map, surface operations

Map Filter can be started from the Volume Data section of the Tools menu and manipulated like other panels (more...). The Map to filter should be chosen from the pulldown menu of volume models already open in ChimeraX.

Filter type:

• Gaussian – convolute the data with a Gaussian function to attenuate high frequencies and smooth the map. This improves the ratio of signal to noise but reduces resolution. It is fastest for data sizes that are powers of 2, and can be very slow when insufficient memory is available. It may be helpful to limit the input to just a subsample or subregion of the original data (see the options). Although it uses a fast Fourier transform calculation method, it does not use map periodicity. Values outside the map boundaries are treated as zero.
• Width – standard deviation of the 3D isotropic Gaussian function in the physical distance units of the map, typically Å. To specify different widths along X, Y, and Z axes, use the volume gaussian command instead.

• Sharpen – perform B-factor sharpening; amplify high frequencies by dividing by a Gaussian in frequency space
• B-factor – the B-factor B2), which is related to the standard deviation σ (Å) of the real-space Gaussian function according to B = 8π2σ2. Sharpening with σ values smaller than the pixel size is most useful; larger values overemphasize high frequencies, in effect amplifying noise. To specify different widths along X, Y, and Z axes, use the volume sharpen command instead.

• Median 3x3x3 – smooth the data by setting each value to the median of the 27 values in the enclosing 3x3x3 box of grid cells. For different box sizes, use the volume median command instead.
• Iterations – how many cycles of value reassignment to perform

• Bin – reduce data size by averaging the values in NxNxN cells of the original data, where N is the Bin size. Different bin sizes along the different axes can be specified by entering three numbers separated by spaces.

• Scale – change data values (not grid point locations). When values are both shifted and scaled, the Shift value is applied before the Scale factor.

• Fourier Transform – only the magnitudes of the complex Fourier components are included in the new data set; the phases are discarded and the constant component is set to zero. The box containing the Fourier transform (with axes in units of reciprocal space) is centered on the original data and scaled to have the same total volume. Some properties of the original data are evident from the Fourier transform. High-frequency components are near the edges of the box, low-freqency components near the center. Volume data is typically oversampled (voxel size two to three times smaller than the actual data resolution) and this causes the Fourier transform to have nonzero values only in the middle half or third of its bounding box. The missing wedge in electron microscope tomograms can also be seen. Spikes radiating along the principal axes in the Fourier transform are caused by nonperiodicity of the original data.

• Laplacian – the Laplacian operation is a sum of second derivatives. Laplacian filtering is useful for edge detection but amplifies noise, so it may be necessary to perform smoothing such as Gaussian filtering beforehand. Finite differences v(i-1)-2*v(i)+v(i+1) along each axis are used, and voxels at the edge of the box are set to zero.

• Flatten – scale data values by factor (1 + a*i + b*j + c*k) where i,j,k are the grid indices and a,b,c are calculated to zero out the first moments of the resulting map (make its mass balance at the center of the grid)
Clicking Filter performs the filtering and creates a new volume model with the result, except if the same type of filtering is applied repeatedly on the same input, the output map is simply replaced. Close simply dismisses the dialog, and Help shows this page in the Help Viewer.

The Options button shows/hides additional options:

• Use displayed subregion – whether to limit the procedure to the current display region (which could be a subregion of the map)
• Use displayed step size – whether to use only the displayed subsample (when step > 1) instead of the full resolution of the current set
• Adjust threshold for constant volume – adjust the contour level on the result to enclose the same volume as the contour surface of the input map
• Immediate update – update the result as soon as a slider parameter (Gaussian width or sharpening B-factor) is changed
• Value type – output value type for Gaussian, sharpening, and scaling operations, with choices: same type as the input map, 8-, 16-, or 32-bit signed integer (int8, int16, or int32), 8-, 16-, or 32-bit unsigned integer (uint8, uint16, or uint32), or 32- or 64-bit floating-point (float32 or float64). The median and binning filters always generate the same value type as the input map, whereas Fourier and Laplacian operations always generate float32.

UCSF Resource for Biocomputing, Visualization, and Informatics / June 2023