Applications/FeatureColorMapper

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FeatureColorMapper Plugin

Screenshot-FeatureColorMapper.png

Short Description

The FeatureColorMapper allows to map feature values extracted for regions in an image onto corresponding label images for visualization.
The features values (like for example extracted by the PaCeQuant plugin) have to be provided as CSV files.
The mapper allows to select a set of features, and for each feature color maps with user-defined colors showing the overlay
of region-specific feature values over the image regions are saved to individual folders on disk.

Release Notes

The FeatureColorMapper is available in MiToBo since release version 1.8.17.

Related Publication

When using the mapper, please cite us:

  • B. Möller, M. Glaß, D. Misiak, and S. Posch, MiToBo - a toolbox for image processing and analysis. In Journal of Open Research Software, 4(1):e17, 2016.

Name of Plugin/Operator

de.unihalle.informatik.MiToBo.apps.cellMorphology.FeatureColorMapper
(available since MiToBo version 1.8.17)

Main features

  • allows to map region features, for example cell features extracted by PaCeQuant, in heatmap style to image regions
  • the color map can be configured by the user in terms of colors used for minimal and maximal values
  • multiple features can be mapped in a single plugin run
  • a range of valid region sizes can be specified to exclude too small or too large regions from processing and mapping

Usage

To run the plugin perform the following steps:

  • install MiToBo by following the instructions on the Installation page
  • run MiToBo and start the operator runner by selecting the menu item MiToBo Runner from Plugins -> MiToBo
  • in the selection menu navigate to de.unihalle.informatik.MiToBo.apps.cellMorphology and select the operator FeatureColorMapper

This will bring up the operator window of the mapper (see figure on the right, top) where the basic configuration parameters can be specified.

You first need to select a folder where the mapper can find feature data that should be mapped. Select the folder using the Choose... button. After selecting a suitable directory, press the Load button . The mapper will search for files with CSV feature data and parse the first of these files to figure out which features are present. These will be listed in the Column(s) to map menu below and can be selected for mapping by the user.
Once the desired features are selected you can specify the color range that should be used and minimal and maximal size thresholds for regions to be considered.
Press the Run button to start the operator.

Input Parameters
Parameter Name Explanation
Input Data Folder where to find the feature data and the set of features to be mapped. Note that the input folder and all its sub-folders are included.
Color Range Minimum Color to which the minimal value of each selected feature is mapped. Between the minimal and maximal color a linear interpolation of values takes place.
Color Range Maximum Color to which the maximal value of each selected feature is mapped. Between the minimal and maximal color a linear interpolation of values takes place.
Minimal Size Threshold Threshold on the size of the regions to be considered; smaller regions are excluded. The unit for the threshold is the same as the unit of the region areas in the feature files.
Maximal Size Threshold Threshold on the size of the regions to be considered; larger regions are excluded. The unit for the threshold is the same as the unit of the region areas in the feature files.
Output Parameters

... coming soon

Sample data

... coming soon