https://github.com/MontpellierRessourcesImagerie/imagej_macros_and_scripts/wiki/Wound-Healing-Tool

The MRI Wound Healing 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. An example image for the find-edges method (see below) can be found here.

Getting Started

To install the tools, drag the link MRI_Wound_Healing_Tool.ijm to the ImageJ launcher window, save it under macros/toolsets in the ImageJ installation and restart ImageJ.

Select the MRI Wound Healing Tool toolset from the >> button of the ImageJ launcher.

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

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

• method: You can choose between a variance based method and a method based on find edges. Note that for find edges the parameters variance-filter-radius and threshold are not taken into account.
• variance filter radius: The radius of the variance filter that is applied to separate the zone occupied by tissue from the empty zone. The radius must be big enough so that the variance due to the tissue plays a role compared to the variance of the noise in the image. Note that the calculation time becomes longer with a bigger radius.
• threshold The image resulting from the variance filter is converted to a mask by applying the given threshold. If the input images are 16bit the threshold 1 will probably work.
• radius open This operation will close holes in the tissue. It must be big enough to close small holes in the tissue and small enough to not close the area of the wound in later images.
• min. size Minimum size from which on the wound is taken into account. This excludes small remaining holes in the tissue.
• ignore spatial calibration If checked the measurements will be in pixel otherwise the spatial calibration of the image if any is used.

• In ImageJ, select Analyze>Set Measurements to select the features you want to measure. You should at least select area and Display label.
• It can happen that the result at one time-point consists of more then one area. You can recognize it because they have the same number in the column slice of the results table. To get the total area for one time-point you need to add all the surfaces measured for that time-point
• Make sure that the option Black background is set in dialog accesible via the menu Process>Binary>options.... Without this option the tool will not work correctly.