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Tool: Segment Map

Segment Map partitions volume data to create a surface model with one or more segmentation regions shown in different colors. Along with the Fit to Segments tool, Segment Map is part of the Segger package described in:

Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. Pintilie GD, Zhang J, Goddard TD, Chiu W, Gossard DC. J Struct Biol. 2010 Jun;170(3):427-38.

Comparison of Segger and other methods for segmentation and rigid-body docking of molecular components in cryo-EM density maps. Pintilie G, Chiu W. Biopolymers. 2012 Sep;97(9):742-60.

Segmentation regions can be measured with Measure and Color Blobs and saved as an index map with segger exportmask.

For interactive (manual) segmentation of medical images, see the Segmentations tool. See also: Volume Viewer, Map Eraser, Map Filter, color zone, volume mask, segmentation, EMDB segmentation file format (SFF), Segger website, Chimera-Segger how-to (2010)


Segment Map performs watershed segmentation: a density map is partitioned so that each local maximum has its own region, and the boundaries between regions lie at the valleys between the local maxima. The goal is usually one region per protein or domain, but the initial segmentation often gives more numerous and smaller regions than desired, especially if the data are noisy. Segger provides various ways to combine regions after the initial segmentation:


It may be necessary to process a density map beforehand for the segmentation to finish in a reasonable amount of time. A map of size 2563 can have a million local maxima if it is noisy. Gaussian smoothing to reduce the number of local maxima can be performed with the command volume gaussian. Gaussian filtering reduces resolution to about six times the Gaussian standard deviation. After smoothing, it will also improve performance to reduce the size of the map with volume bin. For visualization and analysis, it is desirable for a density map to be oversampled by three times in each dimension, so binning should aim for a grid spacing of approximately twice the Gaussian standard deviation.

If interactive rotation speed is poor after segmentation, see response time.

Dialog and Basic Usage

Segment Map can be started from the Volume Data section of the Tools menu (more...).

The map of interest should be chosen from the pulldown menu of open volume data sets next to Segment map. The threshold (contour level) of the map should be adjusted before segmentation, because the calculation will use only the voxels with density values above that level.

Clicking Segment partitions the chosen map by the watershed method plus smoothing and grouping as specified in the segmenting options. The segmentation result is shown as a surface model with one or more segmentation regions of different colors. The resulting number of regions is reported in the dialog and the Log. The segmentation is given the same name as the corresponding map except with .seg appended.

The Current segmentation is indicated in the dialog and can be changed by choosing a different segmentation name from the pulldown menu. Designating a segmentation as the current segmentation shows it and hides any others. Grouping and ungrouping operations modify the current segmentation model rather than creating a new one. However, multiple segmentation models can be open at the same time, and may have been generated from different density maps or opened from previously saved segmentation files.

Grouping and ungrouping can be specified interactively by selection. With default mouse-button assignments, Ctrl-click selects a region and Shift-Ctrl-click selects additional regions without erasing the pre-existing selection.

Segmentation region selection, showing/hiding, and other manipulations can also be performed with the shortcuts options or the Segment Map Regions menu.

Segmentation results are included in saved sessions. They can also be saved separately using the Segment Map File menu or the save command.

Clicking Fit opens the Fit to Segments tool. Clicking Help shows this page in the Help Viewer.

Segmenting Options:

Shortcuts Options:

Segment Map Menu

Menu entries apply only to the current segmentation unless stated otherwise.



Response Time

High number of surface triangles. The number of surface triangles can be reduced by increasing the granularity (triangle size). Doubling the value will reduce the number of triangles by approximately a factor of 4 and may improve rendering speed by a similar factor. The display can also be limited to a specified maximum number of regions.

Selected surfaces. ChimeraX shows selections with outlines, which increase the time to draw a frame. Clearing a selection when it is not needed improves performance.

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