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Merge pull request #13 from MedVIC-Lab/individual-publication-pages
Individual publication pages
2 parents e8b3e3a + 3d74dab commit 045644a

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‎.vitepress/theme/custom.css

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- **Often, !important is required to override the default styles.
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*/
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/* Header */
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.VPNavBarTitle .title {
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font-size: 1.75em !important;
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}
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.VPNavBarMenuLink {
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font-size: 1.05em !important;
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}
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/* Container widths */
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@media (min-width: 1440px) {
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.VPDoc:not(.has-sidebar) .content {

‎README.md

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```markdown
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---
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layout: publication
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title: "Publication Title"
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authors: "Author1, Author2"
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conference: "Conference Name"
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year: "Year"
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link: "https://example.com/publication-link" # Optional: Replace with the URL to the publication
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links:
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archive: "example.com" (optional)
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code: "example.com" (optional)
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publisher: "example.com" (optional)
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pdf: "example.com" (optional)
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video: "example.com" (optional)
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image:
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src: "example.png"
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alt: "Example Alt Text"
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---
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```
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Note: images should be added to `/public/assets/images/publications/`. These should be *graphical abstracts* and should not contain captions.
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Note: images should be added to `/public/assets/images/publications/`.
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Additional note: Images should be *graphical abstracts* and should not contain captions.
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3. **Add content to your Markdown file:** (WORK IN PROGRESS)
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- Below the frontmatter, add any additional information about the publication.

‎layouts/publication.vue

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<template>
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<div>
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<h1>{{ frontmatter.title }}</h1>
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<p>{{ frontmatter.authors }}</p>
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<p>{{ frontmatter.conference }}</p>
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<p>{{ frontmatter.year }}</p>
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<div class="publication-layout vp-doc">
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<div class="publication-content">
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<img v-if="frontmatter.image" :src="`../../assets/images/publications/${frontmatter.image.src}`" :alt="frontmatter.image.alt" class="publication-image" />
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<Content />
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</div>
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<aside class="publication-sidebar">
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<div class="publication-links">
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<h2>Resources</h2>
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<ul>
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<li v-if="frontmatter.links.code"><a :href="frontmatter.links.code" target="_blank"><v-icon size="16" icon="mdi-code-braces"/>Link to Code</a></li>
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<li v-if="frontmatter.links.pdf"><a :href="frontmatter.links.pdf" target="_blank"><v-icon size="16" icon="mdi-file-document-outline"/>Publication (PDF)</a></li>
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<li v-if="frontmatter.links.archive"><a :href="frontmatter.links.archive" target="_blank"><v-icon size="16" icon="mdi-archive"/>Archive</a></li>
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<li v-if="frontmatter.links.video"><a :href="frontmatter.links.video" target="_blank"><v-icon size="16" icon="mdi-video-box"/>Link to Video</a></li>
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<li v-if="frontmatter.links.publisher"><a :href="frontmatter.links.publisher" target="_blank"><v-icon size="16" icon="mdi-earth"/>Link to Publisher</a></li>
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</ul>
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</div>
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</aside>
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</div>
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</template>
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<script setup>
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import { useData } from 'vitepress';
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const { frontmatter } = useData();
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</script>
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import { Content, useData } from 'vitepress';
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const { frontmatter } = useData();
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</script>
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<style>
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.publication-layout {
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display: flex;
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flex-direction: row;
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justify-content: space-between;
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max-width: 1200px; /* Adjust to match the default layout container width */
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margin: 0 auto;
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padding: 20px;
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min-height: 100vh; /* Ensure the layout stretches to the full height of the screen */
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}
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.publication-content {
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flex: 1;
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padding-right: 20px;
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}
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.publication-sidebar {
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width: 300px;
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padding-left: 20px;
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display: flex;
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flex-direction: column;
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justify-content: flex-start;
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}
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.publication-sidebar h2 {
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border-top: 0 !important;
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padding: 0;
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margin: 0;
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}
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.publication-image {
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max-width: 100%;
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margin-bottom: 20px;
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}
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.publication-links ul {
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list-style-type: none;
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padding: 0;
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}
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.publication-links li {
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margin-bottom: 10px;
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}
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</style>

‎pages/publications.md

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display: flex;
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flex-direction: row;
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margin-bottom: 20px;
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text-decoration: none !important;
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border-radius: 10px;
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}
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.publication:hover {
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background-color:rgb(245, 245, 245);
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color: #000!important;
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}
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.publication img {
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display: inline-block;
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}
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</style>
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<span></span>
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<v-row
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justify="space-between"
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class="mb-4"
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</v-row>
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<div class="container">
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<div v-for="publication in sortedPublications" :key="publication.title" class="publication">
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<a v-for="publication in sortedPublications" :key="publication.title" :href="publication.link" class="publication">
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<img v-if="publication.image" :src="`../assets/images/publications/${publication.image.src}`" :alt="publication.image.alt">
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<div class="publication-info">
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<p>{{ publication.authors }}</p>
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<a :href="publication.link" target="_blank">{{ publication.title }}</a>
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<p>{{ publication.title }}</p>
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<p>{{ publication.conference }} ({{ publication.year }})</p>
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</div>
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</div>
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</a>
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</div>

‎pages/publications/2020_uncertain_deepssm.md

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---
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layout: publication
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title: "Uncertain-DeepSSM: From Images to Probabilistic Shape Models"
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authors: "Jadie Adams, Riddhish Bhalodia, Shireen Elhabian. "
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conference: "Shape in Medical Imaging (ShapeMI) at MICCAI"
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year: "2020"
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link: "https://arxiv.org/abs/2007.06516"
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links:
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archive: "https://arxiv.org/abs/2007.06516"
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image:
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src: "2020_uncertain_deepssm.png"
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alt: Results Highlight

‎pages/publications/2021_benchmarking.md

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---
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layout: publication
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title: "Benchmarking Off-the-shelf Statistical Shape Modeling Tools in Clinical Applications"
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authors: "Anupama Goparaju, Krithika Iyer, Alexandre Bône, Nan Hu, Heath B. Henninger, Andrew E. Anderson, Stanley Durrleman, Matthijs Jacxsens, Alan Morris, Ibolya Csecs, Nassir Marrouche, Shireen Y. Elhabian"
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conference: "Medical Image Analysis"
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year: "2021"
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link: "https://www.sciencedirect.com/science/article/pii/S1361841521003169"
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links:
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publisher: "https://www.sciencedirect.com/science/article/pii/S1361841521003169"
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image:
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src: "2021_benchmarking.jpg"
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alt: Benchmarking FrameWork

‎pages/publications/2022_rvtr.md

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---
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layout: publication
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title: "All Roads Lead to Rome: Diverse Etiologies of Tricuspid Regurgitation Create a Predictable Constellation of Right Ventricular Shape Changes"
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authors: "Benjamin A. Orkild, Brian Zenger*, Krithika Iyer*,
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Lindsay C. Rupp, Masjid M. Ibrahim, Atefeh G. Khashani, Maura D. Perez, Markus D. Foote, Jake A. Bergquist, Alan K. Morris, Shireen Elhabian and others"
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conference: "Frontiers in Physiology"
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year: "2022"
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link: "https://www.frontiersin.org/journals/physiology/articles/10.3389/fphys.2022.908552/full"
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links:
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publisher: "https://www.frontiersin.org/journals/physiology/articles/10.3389/fphys.2022.908552/full"
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image:
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src: "2022_rvtr.jpg"
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alt: Results Highlight

‎pages/publications/2022_sharedboundary.md

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---
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layout: publication
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title: "Statistical Shape Modeling of Biventricular Anatomy with Shared Boundaries"
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authors: "Krithika Iyer, Alan Morris, Brian Zenger, Karthik Karnath, Benjamin A. Orkild, Oleksandre Korshak, Shireen Elhabian. "
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conference: "Statistical Atlases and Computational Models of the Heart (STACOM) at MICCAI"
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year: "2022"
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link: "https://pmc.ncbi.nlm.nih.gov/articles/PMC10103081/"
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links:
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publisher: "https://pmc.ncbi.nlm.nih.gov/articles/PMC10103081/"
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image:
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src: "2022_stacom_shared.jpg"
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alt: Results Highlight

‎pages/publications/2022_spatiotemporal_ssm.md

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---
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layout: publication
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title: "Spatiotemporal Cardiac Statistical Shape Modeling: A Data-Driven Approach"
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authors: "Jadie Adams, Nawazish Khan, Alan Morris, Shireen Elhabian"
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conference: "Statistical Atlases and Computational Models of the Heart (STACOM) at MICCAI"
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year: "2022"
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link: "https://arxiv.org/abs/2209.02736"
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links:
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archive: "https://arxiv.org/abs/2209.02736"
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image:
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src: "2022_spatiotemporal_ssm.png"
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alt: Results Highlight

‎pages/publications/2022_vib_deepssm.md

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---
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layout: publication
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title: "From Images to Probabilistic Anatomical Shapes: A Deep Variational Bottleneck Approach"
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authors: "Jadie Adams, Shireen Elhabian"
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conference: "MICCAI"
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year: "2022"
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link: "https://arxiv.org/abs/2205.06862"
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links:
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code: "https://github.com/MedVIC-Lab/VIB-DeepSSM"
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archive: "https://arxiv.org/abs/2205.06862"
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image:
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src: "2022_vib_deepssm.png"
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alt: Results Highlight

‎pages/publications/2023_ADASSM.md

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---
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layout: publication
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title: "ADASSM: Adversarial Data Augmentation in Statistical Shape Models From Images"
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authors: "Mokshagna Sai Teja Karanam, Tushar Kataria, , Krithika Iyer, Shireen Elhabian. "
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conference: "Shape in Medical Imaging (ShapeMI) at MICCAI"
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year: "2023"
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link: "https://arxiv.org/abs/2307.03273"
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links:
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archive: "https://arxiv.org/abs/2307.03273"
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image:
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src: "2023_ADASSM.png"
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alt: Results Highlight

‎pages/publications/2023_Automated_Annotation_pathology.md

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---
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layout: publication
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title: "Automating ground truth annotations for gland segmentation through immunohistochemistry"
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authors: "Tushar Kataria, Saradha Rajamani, Abdul Bari Ayubi, Mary Bronner, Jolanta Jedrzkiewicz, Beatrice S Knudsen, Shireen Y Elhabian"
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conference: "Modern Pathology, Volume 36, Issue 12"
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year: "2023"
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link: "https://www.sciencedirect.com/science/article/pii/S0893395223002363"
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links:
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publisher: "https://www.sciencedirect.com/science/article/pii/S0893395223002363"
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image:
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src: "2023_Automated_Annotation_pathology.png"
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alt: Automated Annotation

‎pages/publications/2023_REU_NSF.md

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---
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layout: publication
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title: "An NSF REU Site Based on Trust and Reproducibility of Intelligent Computation: Experience Report"
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authors: "Mary Hall, Ganesh Gopalakrishnan, Eric Eide, Johanna Cohoon, Jeff Phillips, Mu Zhang, Shireen Elhabian, Aditya Bhaskara, Harvey Dam, Artem Yadrov, Tushar Kataria, Amir Mohammad Tavakkoli, Sameeran Joshi, Mokshagna Sai Teja Karanam"
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conference: "Proceedings of the SC'23 Workshops of The International Conference on High Performance Computing, Network, Storage, and Analysis"
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year: "2023"
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link: "https://dl.acm.org/doi/abs/10.1145/3624062.3624100"
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links:
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publisher: "https://dl.acm.org/doi/abs/10.1145/3624062.3624100"
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---
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# NSF REU Experience Report for 2023

‎pages/publications/2023_SCGAN_virtual_staining.md

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---
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layout: publication
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title: "Structural cycle gan for virtual immunohistochemistry staining of gland markers in the colon"
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authors: "Shikha Dubey,Tushar Kataria, Beatrice S Knudsen, Shireen Y. Elhabian"
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conference: "International Workshop on Machine Learning in Medical Imaging"
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year: "2023"
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link: "https://link.springer.com/chapter/10.1007/978-3-031-45676-3_45"
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links:
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publisher: "https://link.springer.com/chapter/10.1007/978-3-031-45676-3_45"
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image:
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src: "2023_SCGAN_virtual_staining.png"
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alt: Structural CycleGAN

‎pages/publications/2023_benchmarking_pathology_pretraining.md

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---
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layout: publication
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title: "To pretrain or not to pretrain? A case study of domain-specific pretraining for semantic segmentation in histopathology"
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authors: "Tushar Kataria, Beatrice S Knudsen, Shireen Y. Elhabian"
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conference: "Workshop on Medical Image Learning with Limited and Noisy Data"
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year: "2023"
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link: "https://link.springer.com/chapter/10.1007/978-3-031-44917-8_24"
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links:
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code: "https://github.com/MedVIC-Lab/Histopathology-Domain-Specific-Pretraining"
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publisher: "https://link.springer.com/chapter/10.1007/978-3-031-44917-8_24"
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image:
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src: "2023_benchmarking_pathology_pretraining.png"
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alt: Benchmarking Semantic Segmentation

‎pages/publications/2023_benchmarking_segmentation.md

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---
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layout: publication
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title: "Benchmarking Scalable Epistemic Uncertainty Quantification in Organ Segmentation"
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authors: "Jadie Adams, Shireen Elhabian"
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conference: "Unsure Workshop at MICCAI"
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year: "2023"
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link: "https://arxiv.org/abs/2308.07506"
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links:
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archive: "https://arxiv.org/abs/2308.07506"
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image:
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src: "2023_benchmarking_segmentation.png"
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alt: Results Highlight

‎pages/publications/2023_bvib_deepssm.md

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---
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layout: publication
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title: "Fully Bayesian VIB DeepSSM"
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authors: "Jadie Adams, Shireen Elhabian"
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conference: "MICCAI"
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year: "2023"
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link: "https://arxiv.org/pdf/2305.05797.pdf"
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links:
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code: "https://github.com/MedVIC-Lab/BVIB-DeepSSM"
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archive: "https://arxiv.org/pdf/2305.05797.pdf"
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image:
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src: "2023_bvib_deepssm.png"
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alt: Results Highlight

‎pages/publications/2023_can_pointclouds.md

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---
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layout: publication
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title: "Can point cloud networks learn statistical shape models of anatomies?"
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authors: "Jadie Adams, Shireen Elhabian"
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conference: "MICCAI"
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year: "2023"
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link: "https://arxiv.org/abs/2305.05610"
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links:
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code: "https://github.com/MedVIC-Lab/PointCompletionSSM"
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archive: "https://arxiv.org/abs/2305.05610"
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image:
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src: "2023_can_pointclouds.png"
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alt: Results Highlight

‎pages/publications/2023_frontiers_sharedboundary.md

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---
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layout: publication
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title: "Statistical Shape Modeling of Multi-Organ Anatomies with Shared Boundaries: A Data-Driven Approach"
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authors: "Krithika Iyer, Alan Morris, Brian Zenger, Karthik Karnath, Nawazish Khan, Benjamin A. Orkild, Oleksandre Korshak, Shireen Elhabian"
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conference: "Frontiers in Bioengineering and Biotechnology"
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year: "2023"
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link: "https://www.frontiersin.org/journals/bioengineering-and-biotechnology/articles/10.3389/fbioe.2022.1078800/full"
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links:
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publisher: "https://www.frontiersin.org/journals/bioengineering-and-biotechnology/articles/10.3389/fbioe.2022.1078800/full"
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image:
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src: "2023_frontiers_shared.jpg"
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alt: Results Highlight

‎pages/publications/2023_frontiers_spatiotemporal_ssm.md

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---
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layout: publication
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title: "Learning Spatiotemporal Statistical Shape Models for Non-Linear Dynamic Anatomies"
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authors: "Jadie Adams, Nawazish Khan, Alan Morris, Shireen Elhabian"
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conference: "Frontiers in Bioengineering and Biotechnology"
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year: "2023"
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link: "https://www.frontiersin.org/journals/bioengineering-and-biotechnology/articles/10.3389/fbioe.2023.1086234/full"
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links:
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publisher: "https://www.frontiersin.org/journals/bioengineering-and-biotechnology/articles/10.3389/fbioe.2023.1086234/full"
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image:
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src: "2023_frontiers_spatiotemporal_ssm.jpg"
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alt: Results Highlight

‎pages/publications/2023_mesh2ssm.md

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---
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layout: publication
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title: "Mesh2SSM: From Surface Meshes to Statistical Shape Models of Anatomy"
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authors: "Krithika Iyer and Shireen Elhabian"
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conference: "MICCAI 2023"
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year: "2023"
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link: "https://scholar.google.com/citations?view_op=view_citation&hl=en&user=MN0NWL0AAAAJ&citation_for_view=MN0NWL0AAAAJ:W7OEmFMy1HYC"
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links:
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code: "https://github.com/MedVIC-Lab/mesh2SSM_2023"
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archive: "https://arxiv.org/abs/2305.07805"
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image:
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src: "2023_mesh2ssm.png"
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alt: Mesh2SSM Model

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