Up: Component summary
Up: Component summary
Component
SegmentCRImageSegments a directory of images with a method tuned for HE images.
Method described in "Quantitative Image Analysis of Cellular Heterogeneity in Breast Tumors Complements Genomic Profiling" by Y. Yuan, H. Failmezger, O. M. Rueda, H. R. Ali, S. Graf, S.-F. Chin, R. F. Schwarz, C. Curtis, Mark J. Dunning, Helen Bardwell, Nicola Johnson, Sarah Doyle, Gulisa Turashvili, Elena Provenzano, Sam Aparicio, Carlos Caldas and Florian Markowetz - November 21, 2012
| Version | 1.0 |
|---|---|
| Bundle | anima |
| Categories | |
| Authors | Ville Rantanen (ville.rantanen@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | R ; libtiff5-dev (DEB) ; libfftw3-dev (DEB) ; EBImage (R-package) ; CRImage (R-package) |
| Source files | component.xml segment.crimage.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| in | ImageList | Mandatory | A directory with image files. |
Outputs| Name | Type | Description |
|---|---|---|
| mask | ImageList | BW PNG images. |
| perimeter | ImageList | BW PNG images of the perimeter of the mask. |
| features | CSV | Featured measured from images. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| failureRegion | float | 2000 | Dark regions which exceed this value will be deleted |
| maxArea | float | 800 | Maximum accepted pixel area in all methods. |
| method | string | "Otsu" | Method for image segmentation. Choose from 'Otsu', 'Phansalkar'. |
| minArea | float | 1 | Minimum accepted pixel area in all methods. |
| numWindows | int | 5 | Number of separate thresholdings |
Test cases| Test case | Parameters▼ | IN in |
OUT mask |
OUT perimeter |
OUT features |
|---|---|---|---|---|---|
| test1_basic | (missing) | in | mask | perimeter | features |