The 3D dataset, consisting of 128 transaxial slices through the long axis of the kiwi, was acquired with the 7 T Bruker Pharmascan MRI scanner at the MIC / Vivarium, University of Bergen, using the 2D RARE pulse sequence (Echo Train Length = 8, TR = 18520 ms, TE = 63.9 ms, No. of Averages = 2, Flip Angle = 180 deg, Slice thickness = 0.5 mm, In-plane pixel resolution = 0.234 x 0.234 mm^2, Acquisition matrix = 256 x 256, Number of slices = 128).
Segment the seeds from the background using all the clever tricks / ideas you can come up with (e.g. adaptive thresholding, template matching / a priori information, Fourier space methods, …). Try out both 2D and 3D approaches. [Use PYTHON, JAVA (ImageJ/Fiji/MIPAV or MATLAB or …]
Write a short scientific report from your investigation, with a Title, an “Introduction” with problem formulation, “Materials and methods” regarding test object (kiwifruit), image acquisition and the image analysis methods being used (your algorithm / code can be given in an Appendix); “Experimental results” (seed counts for given algorithmic parameter settings, processing time, etc., use Figures and Tables to describe your results); “Discussion” (main results, strength and weaknesses of your approach, suggestions for improvement, relevance to similar problems, conclusions). “Bibliography” (try to find some relevant literature to this image analysis task, and your algorithmic approach). Report should be sent by e-mail at latest on the day before the 2nd period of the course.