Additional file 1.

The computer program, called CellSegmentation3D, loads the 3D Analyze format image (the suffix ".img" or ".hdr" is not needed in the input image name), and the segmentation result is also saved as the Analyze format. For each 3D input image, the program will output two results: 1) the segmentation result, in which all voxels belonging to the same cell are labelled with the same unique intensity; 2) the boundary map that separates segmented cells. Usage: CellSegmentation3D image_Input -f fusion_threshold -m min_Region -d diffusion_iteration -s sigma; Default parameters: fusion_threshold 3, min_Region 50, diffusion_iteration 15, sigma 1.0; For example: CellSegmentation3D elegans-01-01 -f 3 -m 35. This will produce the two result images: elegans-01-01_edge.img and elegans-01-01_segmentation.img. Notes that the segmentation results can be inspected by many visualization tools, provided that they can load 3D Analyze format images. The NIH ImageJ progam (freely downloadable at: http://rsb.info.nih.gov/ij/ webcite) is recommended.

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Li et al. BMC Cell Biology 2007 8:40   doi:10.1186/1471-2121-8-40