This is Hight-Throughput Microscopy Wound healing tool to perform an automatic segmentation and recognition of empty gap for in vitro Wound healing a.k.a "Scratch assay". This tool is supported under terms of Ministry of Education of Republic of Kazakhstan Grant # FDCRG 240919FD3937 (Nazarbayev University) to Ivan Vorobyev.
The tool requires MatLab2014 or higher with Simulink, Image Processing and Mapping Toolbox to run.
After the initialization of tool it requires from user to set path for folder with data and an path for output. The data must be organized as a folder with image sequence or subfolder(s) with an image seuence in. The input image format must be TIFF, PNG or JPG. The output path can be set in the same folder, by default it will set the system default. The result will be mirrored structure of input folder with data files and B&W images of binary mask. As an option the image with oulined gap overlay available (string 217-219 must be active). The WH_area.xlx contain counts of gap in pixel for every frame as a column in ascending order. ImMeanBulk.txt, ImMedBulk.txt and ImStdBulk.txt contain image mean, image median and image standart deviation of image after filtration.
Input
-Data folder
--Folder with image sequence 1
--Folder with image sequence 2
--Folder with image sequence 3
...
--Folder with image sequence n
Output
Path name_Data folder
--Folder with image sequence 1
---bin
--Folder with image sequence 2
---bin
--Folder with image sequence 3
---bin
...
--Folder with image sequence n
---bin
Processing parameters
There is only treshold to be set for processing. Threshold is defined as a fraction of mean and set by a coeficient which must be non-zero positive integer. The default parameter is 3.14 (Pi). The other parameters is listed in the coments within the script.
Results
The results is a pixel count of area gap in a middle of image. The user then can convert pixel counts to metric units according to microscope scale.
Examples of processing
Images are obtained from TScratch test set, 8-bit grayscale, objective magnification: NA, detector: NA
set of binary masks
set of wound contour overlays
Images are obtained from WH_Macro_tool test set, 16-bit grayscale, objective magnification: NA, detector: NA
set of binary masks
set of wound contour overlays
The link to the stable 3rd party tools
- For TScratch https://github.com/cselab/TScratch
- For MRI Wound Healing Tool by Volker Baecker https://github.com/MontpellierRessourcesImagerie/imagej_macros_and_scripts/wiki/Wound-Healing-Tool