Measuring hidden phenotype: quantifying the shape of barley seeds using the Euler characteristic transform

Shape plays a fundamental role in biology. Traditional phenotypic analysis methods measure some features but fail to measure the information embedded in shape comprehensively. To extract, compare and analyse this information embedded in a robust and concise way, we turn to topological data analysis (TDA), specifically the Euler characteristic transform. TDA measures shape comprehensively using mathematical representations based on algebraic topology features. To study its use, we compute both traditional and topological shape descriptors to quantify the morphology of 3121 barley seeds scanned with X-ray computed tomography (CT) technology at 127 μm resolution. The Euler characteristic transform measures shape by analysing topological features of an object at thresholds across a number of directional axes. A Kruskal–Wallis analysis of the information encoded by the topological signature reveals that the Euler characteristic transform picks up successfully the shape of the crease and bott..., We selected 28 barley accessions with diverse spike morphologies and geographical origins for our analysis (Harlan and Martini 1929, 1936, 1940). In November of 2016, seeds from each accession were stratified at 4C on wet paper towels for a week, and germinated on the bench at room temperature. Four day old seedlings were transferred into pots in triplicate and arranged in a completely randomized design in a greenhouse. Day length was extended throughout the experiment using artificial lighting ---minimum 16h light / 8h dark. After the plants reached maturity and dried, a single spike was collected from each replicate for scanning at Michigan State University.The scans were produced using the North Star Imaging X3000 system and the included efX software, with 720 projections per scan, with 3 frames averaged per projection. The data was obtained in continuous mode. The X‐ray source was set to a voltage of 75 kV, current of 100 μA, and focal spot size of 7.5μm. The 3D recons..., X-ray CT scan images are provided for 774 individual barley panicle and their corresponding 37 881 clean, individual seeds. All the scans are provided as single 3D 8-bit TIFF files. Three raw X-ray CT scans containing 4 barley panicles each are included as well. The code developed to process these scans and segment out the panicles and seeds is provided as well. The code is written as commented jupyter notebooks, using both python and R.
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