Up: Component summary Component

IntensityFeatures

Extracts the intensity features from segmented image mask and gray scale image.

Example:

Sources:

Outputs:

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

case2_masklist properties images mask (missing) masklist edges out

erodeWidth=4,
isRatio=true


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