class: center, middle, inverse, title-slide .title[ # When life gives you lemons ] .subtitle[ ## model the citrus oil gland distribution ] .author[ ### <strong>Erik Amézquita</strong> <br> - ] .institute[ ### Computational Mathematics, Science and Engineering <br> Michigan State University <br> - ] .date[ ### 2022-02-19 ] --- class: inverse, center # Scan all (the citrus) <div class="row"> <div class="column" style="max-width:50%"> <iframe width="375" height="210" src="https://www.youtube-nocookie.com/embed/khRS5AuleIM?controls=0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe> <iframe width="375" height="210" src="https://www.youtube-nocookie.com/embed/HAIaektvV3Q?controls=0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe> </div> <div class="column" style="max-width:50%"> <iframe width="375" height="210" src="https://www.youtube-nocookie.com/embed/Xo2HULkkm3s?controls=0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe> <iframe width="375" height="210" src="https://www.youtube-nocookie.com/embed/EwTwSNrBuIo?controls=0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe> </div> </div> --- # Citrus taxonomy is... complicated - 10* _fundamental_ citrus gave rise to all citrus diversity we see today - Originated in South and South East Asia, and Australia. - Still some debate as to what exactly is a citrus .pull-left[  <p style="font-size: 8px; text-align: right; color: Grey;"> Credits: <a href="https://doi.org/10.1038/nature25447">Wu <em>et al.</em> (2018)</a></p> ] .pull-right[  <p style="font-size: 8px; text-align: right; color: Grey;"> Credits: <a href="https://doi.org/10.1038/nature25447">Wu <em>et al.</em> (2018)</a></p> ] --- ## Think of citrus as lego blocks  <p style="font-size: 8px; text-align: right; color: Grey;"> Credits: <a href="https://doi.org/10.1038/nature25447">Wu <em>et al.</em> (2018)</a></p> --- class: inverse, center, middle # Scan it all! ] --- ## Raw Data: X-rays &rarr; Image Processing <div class="row"> <div class="column" style="max-width:38%; color: Navy; font-size: 15px;"> <img style="padding: 2px 0 2px 0;" src="../../citrus/crc_pics/crc_diversity.jpg"> <p style="text-align: center;"> UCR Collaboration </p> </div> <div class="column" style="max-width:38%; color: Navy; font-size: 15px;"> <img style="padding: 2px 0 2px 0;" src="../../citrus/crc_pics/citrus_xrayct_scanning.jpeg"> <p style="text-align: center;"> 3D X-Ray CT scan </p> </div> <div class="column" style="max-width:23%; color: Navy; font-size: 15px;"> <img src="../../citrus/figs/SR01_CRC3289_12B-19-9_L01_raw.gif"> <p style="text-align: center;"> Raw </p> </div> </div> -- <div class="row" style="margin: 0 auto;"> <div class="column" style="max-width:20%; color: Navy; font-size: 15px;"> <img src="../figs/SR01_L01_black_spine.gif"> <p style="text-align: center;"> Spine </p> </div> <div class="column" style="max-width:20%; color: Navy; font-size: 15px;"> <img src="../figs/SR01_L01_black_endocarp.gif"> <p style="text-align: center;"> Endocarp </p> </div> <div class="column" style="max-width:20%; color: Navy; font-size: 15px;"> <img src="../figs/SR01_L01_black_rind.gif"> <p style="text-align: center;"> Rind </p> </div> <div class="column" style="max-width:20%; color: Navy; font-size: 15px;"> <img src="../figs/SR01_L01_black_exocarp.gif"> <p style="text-align: center;"> Exocarp </p> </div> <div class="column" style="max-width:20%; color: Navy; font-size: 15px;"> <img src="../figs/SR01_L01_black_oil_glands.gif"> <p style="text-align: center;"> Oil glands</p> </div> </div> --- background-image: url("../figs/citrus_diagnostic.gif") background-size: 650px background-position: 50% 70% ## Rich tissue collection --- class: inverse, center, middle # Looking to strike some oil --- # Allometry  --- # Allometry  --- # Allometry  --- background-image: url("../ellipsoids/Li_and_Griffiths_2004.png") background-size: 200px background-position: 95% 3% ## Model the whole fruit as an ellipsoid .pull-left[   ] .pull-right[   ] --- # How round _is_ a round orange?  --- ## Oil gland modeling with directional statistics ### Lambert Azimuthal Projection .pull-left[  <p style="font-size: 8px; text-align: right; color: Grey;"> Credits: <a href="https://en.wikipedia.org/wiki/Lambert_azimuthal_equal-area_projection">Wikipedia</a></p> ] .pull-right[  <p style="font-size: 8px; text-align: right; color: Grey;"> Credits: <a href="https://en.wikipedia.org/wiki/Lambert_azimuthal_equal-area_projection">Wikipedia</a></p> ] Helps to visualize better a sphere in 2D --- background-image: url("../ellipsoids/GarciaPortugues_2013.png") background-size: 250px background-position: 95% 3% ## Spherical Kernel Density Estimation  - Oil glands of a mandarin - Red arrows indicate the most significant gradient values for the density function -- - Statistical tool to model oil gland distribution! --- background-image: url("../figs/SW03_CRC1241-B_12B-4-3_L00_uniform_comparison.jpg") background-size: 600px background-position: 50% 90% ## Distribution of oil glands is NOT uniform --- # Future directions .pull-left[  <p style="font-size: 8px; text-align: right; color: Grey;"> Credits: <a href="https://www.boredpanda.com/life-cycles-pics/">BoredPanda</a></p> Developing cycle of a lemon ] .pull-right[ - Compare differences in oil gland density distribution - Between "species" - Between wild types and domesticated fruits - Propose a distribution model - Insights into fruit development ] --- class: inverse, middle # Thank you! .pull-left[  <p style="font-size: 12px; text-align: right; color: Grey;"> Credits: <a href="https://citrusaustralia.com.au/wp-content/uploads/Citrus-picking-guide.pdf">Citrus Australia</a></p> ] .pull-right[ Joint work with: - Michelle Quigley (MSU Hort) - Tim Ophelders (TU Eidhoven) - Danelle Seymour (UC Riverside) - Liz Munch (MSU CMSE/Math) - Dan Chitwood (MSU Hort/CMSE) <img src="../../img/cmse_logo.svg" width="200" style="display: block; margin: auto;" /> ] -- ### Slides made with [RMarkdown + xaringan](https://bookdown.org/yihui/rmarkdown/xaringan-preview.html)