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Open Access Highly Accessed Methodology article

3D cell nuclei segmentation based on gradient flow tracking

Gang Li12, Tianming Liu13, Ashley Tarokh13, Jingxin Nie12, Lei Guo2, Andrew Mara4, Scott Holley4 and Stephen TC Wong13*

Author Affiliations

1 Center for Bioinformatics, Harvard Center for Neurodegeneration and Repair, Harvard Medical School, Boston, MA, USA

2 School of Automation, Northwestern Polytechnic University, Xi'an, China

3 Functional and Molecular Imaging Center, Department of Radiology, Brigham and Women's Hospital, Boston, MA, USA

4 Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA

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BMC Cell Biology 2007, 8:40  doi:10.1186/1471-2121-8-40

Published: 4 September 2007

Additional files

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.

Format: EXE Size: 232KB Download file

Open Data

Additional file 2:

The elegans-01-01.img is an example image file.

Format: IMG Size: 2.8MB Download file

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Additional file 3:

The elegans-01-01.hdr is the header file associated with the image.

Format: HDR Size: 1KB Download file

Open Data