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Up: Component summary
Component
SegmentFijiProduces binary mask images, segmenting the input images using Fiji. For method selection, see: http://fiji.sc/Auto_Threshold. Append method name with " dark" to invert image first.
| Version | 0.1 |
|---|---|
| Bundle | anima |
| Categories | |
| Authors | Miko Valori (miko.valori@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | Fiji |
| Source files | component.xml fijistart.py fijithreshold.sh |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| in | ImageList | Mandatory | Grayscale input images to be segmented. |
Outputs| Name | Type | Description |
|---|---|---|
| mask | ImageList | Generated masks as .png files |
| perimeter | ImageList | Generated perimeters as .png files |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| corr | float | 1 | Correction coefficient for calculated threshold level |
| display | boolean | false | Set to true to use the current DISPLAY. When false, tries to send screen to Xvfb (if installed), use to debug etc.. |
| method | string | "Otsu" | Method used for setting segmentation threshold |
Test cases| Test case | Parameters▼ | IN in |
OUT mask |
OUT perimeter |
||
|---|---|---|---|---|---|---|
| case1 | properties | in | mask | perimeter | ||
|
corr=0.4, |
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