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Up: Component summary
Component
SegmentGraphCutSegmentation based on graph cutting. Suitable especially for nucleus segmentation.
The component uses a tool found in FARSight: http://www.farsight-toolkit.org/wiki/Nuclear_Segmentation
To produce the result images, ImageMagick is required!
| Version | 1.1 |
|---|---|
| Bundle | anima |
| Categories | Image Processing |
| Authors | Ville Rantanen (ville.rantanen@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | bash ; imagemagick (DEB) ; libqtgui4 (DEB) ; FARSight segment_nuclei ; installer (bash) |
| Source files | component.xml segment_run.sh |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| in | ImageList | Mandatory | A directory with grayscale image files. Images will be converted to 8bit grayscale, you may have to auto-level brightness of 16bit images. |
Outputs| Name | Type | Description |
|---|---|---|
| mask | ImageList | BW PNG images. |
| perimeter | ImageList | BW PNG images of the perimeter of the mask. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| UseDistanceMap | boolean | true | a boolean parameter used to enable the use of the distance constraint to select the LoG scales |
| binary | string | "segment_nuclei" | Binary to use. You can also provide the full path to the binary. |
| continueNext | boolean | true | Continue to next image after failure, or timeout. Produces an empty mask |
| finalizeSegmentation | boolean | true | a boolean parameter used to enable the segmentation refinement step |
| highSensitivity | boolean | false | a boolean parameter used to enable high sensitivity binarization. Default value is false. |
| maxScale | float | 6 | the maximum scale of the Laplacian of Gaussian filter. |
| minScale | float | 4 | the minimum scale of the Laplacian of Gaussian filter. |
| refinementRange | int | 5 | If segmentation finalization (refinement) is enabled, this parameter sets the maximum distance that an initial contour can be shifted |
| samplingRatio | int | 2 | ratio of image sampling along Z to the sampling in X-Y |
| timeout | string | "30m" | Timeout individual image segmentation process. Express as seconds, or with suffixes: s,m,h or d; e.g. "5m" for 5 minutes. |
| xyClusteringRes | int | 2 | resolution of the local maximum clustering (in the x-y plane) used in the initial binarization step |
| zClusteringRes | int | 1 | resolution of the local maximum clustering (along z) used in the initial binarization step |
Test cases| Test case | Parameters▼ | IN in |
OUT mask |
OUT perimeter |
||
|---|---|---|---|---|---|---|
| case1 | properties | in | mask | perimeter | ||
|
minScale=7, |
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