Move from ImageJ to OpenCV
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rkrug commented
I will start the discussion the move from ImageJ to OpenCV.
An initial question in the OpenCV forum indicated that it would be possible to use OpenCV instead of ImageJ.
The process would involve the following steps:
Background identification and removal
Blob detection
https://learnopencv.com/blob-detection-using-opencv-python-c/
binarisation
i.e. converting the moving particles to one colour (necessary?)
morphology
- identification of boundaries
- https://www.tutorialspoint.com/opencv/opencv_morphological_operations.htm
particle tracking
- https://learnopencv.com/object-tracking-using-opencv-cpp-python/
- https://www.pyimagesearch.com/2018/07/30/opencv-object-tracking/
particle measuring
- This could possibly done in R, when the boundaries of the particles are exported?
- This looks promising: https://docs.opencv.org/3.3.1/d3/dc0/group__imgproc__shape.html#ga107a78bf7cd25dec05fb4dfc5c9e765f
- https://docs.opencv.org/3.3.1/dd/d49/tutorial_py_contour_features.html