class: center, middle, inverse, title-slide # Measuring the shape of barley ## using topology ### <strong>Erik Amézquita</strong>, Michelle Quigley, Tim Ophelders <br> Elizabeth Munch, Dan Chitwood <br> Dan Koenig, Jacob Landis <br> - ### Computational Mathematics, Science and Engineering <br> Michigan State University <br> - ### 2021-10-22 --- <div class="row"> <div class="column" style="max-width:44%"> <a href="https://www.bloomberg.com/news/articles/2020-09-13/iraq-to-offer-first-ever-barley-exports-as-rains-yield-surplus" target="_blank"><img style="padding: 0 0 0 0;" src="../figs/barley_iraq.jpg"></a> </div> </div> --- <div class="row"> <div class="column" style="max-width:44%"> <a href="https://www.bloomberg.com/news/articles/2020-09-13/iraq-to-offer-first-ever-barley-exports-as-rains-yield-surplus" target="_blank"><img style="padding: 0 0 0 0;" src="../figs/barley_iraq.jpg"></a> </div> <div class="column" style="max-width:44%"> <a href="https://cereal.interreg-npa.eu/subsites/CEREAL/Barley_cultivation-Norway_Presentation_2018.pdf" target="_blank"><img style="padding: 0 0 0 0;" src="../figs/barley_norway.jpg"></a> </div> </div> --- <div class="row"> <div class="column" style="max-width:44%"> <a href="https://www.bloomberg.com/news/articles/2020-09-13/iraq-to-offer-first-ever-barley-exports-as-rains-yield-surplus" target="_blank"><img style="padding: 0 0 0 0;" src="../figs/barley_iraq.jpg"></a> <a href="https://www.resilience.org/stories/2020-03-09/the-last-crop-before-the-desert/" target="_blank"><img style="padding: 0 0 0 0;" src="../figs/barley_morocco.jpg"></a> </div> <div class="column" style="max-width:44%"> <a href="https://cereal.interreg-npa.eu/subsites/CEREAL/Barley_cultivation-Norway_Presentation_2018.pdf" target="_blank"><img style="padding: 0 0 0 0;" src="../figs/barley_norway.jpg"></a> </div> </div> --- <div class="row"> <div class="column" style="max-width:44%"> <a href="https://www.bloomberg.com/news/articles/2020-09-13/iraq-to-offer-first-ever-barley-exports-as-rains-yield-surplus" target="_blank"><img style="padding: 0 0 0 0;" src="../figs/barley_iraq.jpg"></a> <a href="https://www.resilience.org/stories/2020-03-09/the-last-crop-before-the-desert/" target="_blank"><img style="padding: 0 0 0 0;" src="../figs/barley_morocco.jpg"></a> </div> <div class="column" style="max-width:44%"> <a href="https://cereal.interreg-npa.eu/subsites/CEREAL/Barley_cultivation-Norway_Presentation_2018.pdf" target="_blank"><img style="padding: 0 0 0 0;" src="../figs/barley_norway.jpg"></a> <a href="https://www.tibettravel.org/tibetan-culture/highland-barley.html" target="_blank"><img style="padding: 0 0 0 0;" src="../figs/barley_seed_tibet.jpg"></a> </div> </div> --- <div class="row"> <div class="column" style="max-width:44%"> <a href="https://www.bloomberg.com/news/articles/2020-09-13/iraq-to-offer-first-ever-barley-exports-as-rains-yield-surplus" target="_blank"><img style="padding: 0 0 0 0;" src="../figs/barley_iraq.jpg"></a> <a href="https://www.resilience.org/stories/2020-03-09/the-last-crop-before-the-desert/" target="_blank"><img style="padding: 0 0 0 0;" src="../figs/barley_morocco.jpg"></a> <a href="https://www.nationalgeographic.co.uk/travel/2020/05/photo-story-from-barley-fields-to-whisky-barrels-in-rural-scotland" target="_blank"><img style="padding: 0 0 0 0;" src="../figs/barley_seed_scotland_cropped.jpg"></a> </div> <div class="column" style="max-width:44%"> <a href="https://cereal.interreg-npa.eu/subsites/CEREAL/Barley_cultivation-Norway_Presentation_2018.pdf" target="_blank"><img style="padding: 0 0 0 0;" src="../figs/barley_norway.jpg"></a> <a href="https://www.tibettravel.org/tibetan-culture/highland-barley.html" target="_blank"><img style="padding: 0 0 0 0;" src="../figs/barley_seed_tibet.jpg"></a> </div> </div> --- <div class="row"> <div class="column" style="max-width:44%"> <a href="https://www.bloomberg.com/news/articles/2020-09-13/iraq-to-offer-first-ever-barley-exports-as-rains-yield-surplus" target="_blank"><img style="padding: 0 0 0 0;" src="../figs/barley_iraq.jpg"></a> <a href="https://www.resilience.org/stories/2020-03-09/the-last-crop-before-the-desert/" target="_blank"><img style="padding: 0 0 0 0;" src="../figs/barley_morocco.jpg"></a> <a href="https://www.nationalgeographic.co.uk/travel/2020/05/photo-story-from-barley-fields-to-whisky-barrels-in-rural-scotland" target="_blank"><img style="padding: 0 0 0 0;" src="../figs/barley_seed_scotland_cropped.jpg"></a> </div> <div class="column" style="max-width:44%"> <a href="https://cereal.interreg-npa.eu/subsites/CEREAL/Barley_cultivation-Norway_Presentation_2018.pdf" target="_blank"><img style="padding: 0 0 0 0;" src="../figs/barley_norway.jpg"></a> <a href="https://www.tibettravel.org/tibetan-culture/highland-barley.html" target="_blank"><img style="padding: 0 0 0 0;" src="../figs/barley_seed_tibet.jpg"></a> <a href="https://www.doi.org/10.1007/978-1-4419-0465-2_2168" target="_blank"><img style="padding: 0 0 0 0;" src="../figs/barley_world.jpg"></a> </div> <div class="column" style="max-width:8%; font-size: 15px;"> <p style="text-align: center; font-size: 30px; line-height: 1em; color:#18453B"> <strong> Barley across the world:<br><br>28 different accessions</strong></p> </div> </div> --- # Raw Data: X-rays → Image Processing <div class="row"> <div class="column" style="max-width:37.5%; color: Navy; font-size: 15px;"> <img style="padding: 2px 0 2px 0;" src="../figs/barley_packing.jpg"> <p style="text-align: center;">Barley shipped from California</p> </div> </div> --- # Raw Data: X-rays → Image Processing <div class="row"> <div class="column" style="max-width:37.5%; color: Navy; font-size: 15px;"> <img style="padding: 2px 0 2px 0;" src="../figs/barley_packing.jpg"> <p style="text-align: center;">Barley shipped from California</p> </div> <div class="column" style="max-width:50%; color: Navy; font-size: 15px;"> <img src="../figs/x3000_setup.jpg"> <p style="text-align: center;">Proprietary X-Ray CT scan reconstruction</p> </div> </div> --- # Raw Data: X-rays → Image Processing <div class="row"> <div class="column" style="max-width:37.5%; color: Navy; font-size: 15px;"> <img style="padding: 2px 0 2px 0;" src="../figs/barley_packing.jpg"> <p style="text-align: center;">Barley shipped from California</p> </div> <div class="column" style="max-width:50%; color: Navy; font-size: 15px;"> <img src="../figs/x3000_setup.jpg"> <p style="text-align: center;">Proprietary X-Ray CT scan reconstruction</p> </div> </div> <div class="row"> <div class="column" style="max-width:38%; color: Navy; font-size: 15px;"> <img style="padding: 2px 0 2px 0;" src="../figs/barley_xray_setup.jpg"> <p style="text-align: center;">Creative setup</p> </div> </div> --- # Raw Data: X-rays → Image Processing <div class="row"> <div class="column" style="max-width:37.5%; color: Navy; font-size: 15px;"> <img style="padding: 2px 0 2px 0;" src="../figs/barley_packing.jpg"> <p style="text-align: center;">Barley shipped from California</p> </div> <div class="column" style="max-width:50%; color: Navy; font-size: 15px;"> <img src="../figs/x3000_setup.jpg"> <p style="text-align: center;">Proprietary X-Ray CT scan reconstruction</p> </div> </div> <div class="row"> <div class="column" style="max-width:38%; color: Navy; font-size: 15px;"> <img style="padding: 2px 0 2px 0;" src="../figs/barley_xray_setup.jpg"> <p style="text-align: center;">Creative setup</p> </div> <div class="column" style="max-width:17.5%; color: Navy; font-size: 15px;"> <img src="../figs/S019_L0_1.gif"> <p style="text-align: center;"> 975 spikes </p> </div> <div class="column" style="max-width:17%; color: Navy; font-size: 15px;"> <img src="../figs/S017_L3_1.gif"> <p style="text-align: center;"> 28 accessions </p> </div> </div> --- # Raw Data: X-rays → Image Processing <div class="row"> <div class="column" style="max-width:37.5%; color: Navy; font-size: 15px;"> <img style="padding: 2px 0 2px 0;" src="../figs/barley_packing.jpg"> <p style="text-align: center;">Barley shipped from California</p> </div> <div class="column" style="max-width:50%; color: Navy; font-size: 15px;"> <img src="../figs/x3000_setup.jpg"> <p style="text-align: center;">Proprietary X-Ray CT scan reconstruction</p> </div> </div> <div class="row"> <div class="column" style="max-width:38%; color: Navy; font-size: 15px;"> <img style="padding: 2px 0 2px 0;" src="../figs/barley_xray_setup.jpg"> <p style="text-align: center;">Creative setup</p> </div> <div class="column" style="max-width:17.5%; color: Navy; font-size: 15px;"> <img src="../figs/S019_L0_1.gif"> <p style="text-align: center;"> 975 spikes </p> </div> <div class="column" style="max-width:17%; color: Navy; font-size: 15px;"> <img src="../figs/S017_L3_1.gif"> <p style="text-align: center;"> 28 accessions </p> </div> <div class="column" style="max-width:20.5%; color: Navy; font-size: 15px;"> <img src="../figs/S017_L0_seed_10_0.gif"> <p style="text-align: center;"> 38,000 seeds </p> </div> </div> --- ### Shape extraction: Traditional <img src="../figs/barley_seed_traditional.png" width="500" style="display: block; margin: auto;" /> -- ### Topological description: Euler Characteristic Transform (ECT) <img src="../figs/ect_ver2.gif" width="500" style="display: block; margin: auto;" /> -- - [**Theorem** (Turner, Mukherjee, Boyer, 2014)](https://arxiv.org/abs/1310.1030): The ECT is a sufficient statistic in 3D. --- # Hidden topological shape information - **Goal:** Classify 28 barley accessions using solely grain morphology information. -- .pull-left[  ] .pull-right[ <img src="../figs/pole_directions_p7_m12_crop.jpg" width="200" style="display: block; margin: auto;" /> ] --- # Hidden topological shape information - **Goal:** Classify 28 barley accessions using solely grain morphology information. .pull-left[  <img src="../figs/kruskal_wallis_topo_summary.jpg" width="400" style="display: block; margin: auto;" /> ] .pull-right[ <img src="../figs/pole_directions_p7_m12_crop.jpg" width="200" style="display: block; margin: auto;" /> ] --- # Hidden topological shape information - **Goal:** Classify 28 barley accessions using solely grain morphology information. .pull-left[  <img src="../figs/kruskal_wallis_topo_summary.jpg" width="400" style="display: block; margin: auto;" /> ] .pull-right[ <img src="../figs/discerning_directions.png" width="200" style="display: block; margin: auto;" />  ] --- class: right, bottom, inverse background-image: url("../figs/acknowledgments.jpg") background-size: 1000px background-position: 50% 40%