Up: Component summary
Up: Component summary
Component
IntensityFeaturesExtracts the intensity features from segmented image mask and gray scale image.
Example:
Sources:
 |  |
| File | Object | Mean | Median | StDev | Sum | Low 1% | High 1% | Margination | |
| cells.tif_test.png | 1 | 0.09380 | 0.09412 | 0.00702 | 68.0039 | 0.07424 | 0.10598 | 1.02744 | |
| cells.tif_test.png | 2 | 0.54362 | 0.56078 | 0.10123 | 155.475 | 0.25861 | 0.74115 | 1.27216 | |
| cells.tif_test.png | 3 | 0.69176 | 0.69804 | 0.18622 | 419.204 | 0.31355 | 1 | 1.58960 | |
| cells.tif_test.png | 4 | 0.58782 | 0.62353 | 0.16344 | 269.224 | 0.21538 | 0.86276 | 1.44734 | |
| cells.tif_test.png | 5 | 0.71412 | 0.74118 | 0.17285 | 492.027 | 0.34481 | 0.98437 | 1.53338 | |
| cells.tif_test.png | 6 | 0.42481 | 0.41176 | 0.12128 | 379.780 | 0.22320 | 0.71771 | 1.44711 | |
Haralick texture feature extraction algorithm: Haralick et al. (1973), "Textural Features for Image Classification.",% IEEE Transaction on Systems, Man, Cybernetics, SMC-3(6):610-621, with GPL licensed CellProfiler implementation, https://svn.broadinstitute.org/CellProfiler/trunk/CellProfiler_old_matlab/Modules/ (Jones TR, Kang IH, Wheeler DB, Lindquist RA, Papallo A, Sabatini DM, Golland P, Carpenter AE (2008) CellProfiler Analyst: data exploration and analysis software for complex image-based screens. BMC Bioinformatics 9(1):482/doi: 10.1186/1471-2105-9-482. PMID: 19014601 PMCID: PMC2614436)
| Version | 2.3 |
|---|---|
| Bundle | anima |
| Categories | Image Analysis |
| Authors | Ville Rantanen (ville.rantanen@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | Matlab |
| Source files | component.xml imageintensity.m imagesinglefeatures.m CalculateGabor.m CalculateHaralick.m execute.m |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| images | ImageList | Mandatory | A directory with grayscale image files. |
| mask | ImageList | Mandatory | A directory with BW mask image files. |
| names | ImageList | Optional | A directory with the original image files, for naming the table. If omitted, names from "mask" are used. |
| masklist | MaskList | Optional | A MaskList source for the objects. If given, the mask input is not used for objects, but must be given for file names. |
Outputs| Name | Type | Description |
|---|---|---|
| edges | ImageList | A directory with BW mask image files with the erosion mask edge. |
| out | CSV | List of feature values. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| connectivity | int | 4 | Mask object connectivity. 4 or 8. Does not apply if masklist input is used |
| erodeWidth | float | 0 | Erosion width to calculate margination in pixels or percentage of object length. Erosion width can be negative, which means the object will be dilated. |
| isRatio | boolean | false | Eroding width is expressed in percentage of object width instead absolute pixels. |
| percentile | float | 1 | Percentile to read from object intensities. Value 1 equals 1% and 99% will be measured as Low %1 and High 1%. |
| prefix | string | "" | Prefix string for data headers in the result table. Used when reading the same images with multiple parameters and then joining the results. |
| textureScale | float | 1 | Scaling factor for texture features |
Test cases| Test case | Parameters▼ | IN images |
IN mask |
IN names |
IN masklist |
OUT edges |
OUT out |
|---|---|---|---|---|---|---|---|
| case1 | properties | images | mask | (missing) | (missing) | edges | out |
|
erodeWidth=10 |
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| case2_masklist | properties | images | mask | (missing) | masklist | edges | out |
|
erodeWidth=4, |
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