Wound Healing Coherency Tool

The Wound Healing Coherency Tool can be used to analyze scratch assays. It measures the area of a wound in a cellular tissue on a stack of images representing a time-series. An example image can be found here: TimeLapse_2.tif.

Getting Started

The macro needs FeatureJ and MorphoLibJ to be installed. In FIJI they can be installed via the updater by activating the ImageScience update site and the IJPB-plugins site. To install the tools, drag the link Measure_Wound_Healing_Coherency.ijm to the ImageJ launcher window, save it under macros/toolsets in the FIJI installation and restart FIJI.

Select the "Measure_Wound_Healing_Coherency" toolset from the >> button of the ImageJ launcher.

the wound healing coherency toolset

  • the first button opens this help-page.
  • the m button starts the measurement on the active stack

Options

By right-clicking on the m button you can open the options dialog.

the options dialog of the wound healing coherency tool

  • radius close: the radius of the morphological close filter that is applied after a mask has been created
  • radius open: the radius of the morphological open filter that is applied after a mask has been created
  • radius big close: after small objects have been eliminated a close filter with this radius is applied
  • min-size: minimum size of tissue objects that will be taken into account
  • sigma for coherency: to calculate the coherency, "FeatureJ structure" is used to calculate the smallest and largest structure eigenvalues. Sigma is passed to the FeatureJ Structure smoothing parameter.
  • window size for coherency: to calculate the coherency, "FeatureJ structure" is used to calculate the smallest and largest structure eigenvalues. Window size is passed to the FeatureJ Structure integration parameter.

Results

[ result image 1 | result image 2 | result measurements |

See also

Other links

TimeLapse_2.tif - Example image (16 MB) Volker Baecker, 03/20/2017 02:48 PM

toolset.png - the wound healing coherency toolset (985 Bytes) Volker Baecker, 03/20/2017 02:59 PM

options.png - the options dialog of the wound healing coherency tool (10.5 KB) Volker Baecker, 03/20/2017 03:02 PM

res01.png - result image 1 (57.6 KB) Volker Baecker, 03/20/2017 03:28 PM

res02.png - result image 2 (62 KB) Volker Baecker, 03/20/2017 03:28 PM

measurements.png - result measurements (2.39 KB) Volker Baecker, 03/20/2017 03:28 PM

WOUND_CLOSURE_ASSAY_WELL5_PH_POS1_stiped.tif - a larger test dataset (306 MB) Volker Baecker, 09/14/2017 12:19 PM