Wound Healing Coherency Tool - MontpellierRessourcesImagerie/imagej_macros_and_scripts GitHub Wiki

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.

The source code in github can be found here.

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 and save it under macros/toolsets in the FIJI installation.

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

toolset.png

  • 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.

options.png

  • 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

res01.png res02.png measurements.png

See also

Other links

  1. ImageJ practical skills - cell scratch test analysis (plug-in articles) (Chinese) - Instructions of how to install and use the tool.

Publications using the tool

  1. Zhu, M., Deng, X., Zhang, N., Zhang, P., Lai, C., Cai, S., Huang, J., Chen, X., Liu, Y., Zeng, W., Ke, M., 2024. Dexamethasone induces trabecular meshwork cell myofibroblast transdifferentiation through ARHGEF26. The FASEB Journal 38, e23848. 10.1096/fj.202400400RR

  2. Zhou, H., Sun, W. & Zou, J. Analysis of expression profiles and prognostic value of COP9 signalosome subunits for patients with head and neck squamous cell carcinoma. Oncol Lett 22, 803 (2021).

  3. Ye, X., Wei, X., Liao, J., Chen, P., Li, X., Chen, Y., Yang, Y., Zhao, Q., Sun, H., Pan, L., et al. (2021). 4-Hydroxyphenylpyruvate Dioxygenase-Like Protein Promotes Pancreatic Cancer Cell Progression and Is Associated With Glutamine-Mediated Redox Balance. Front. Oncol. 10, 617190.