Merge pull request #17 from MedVIC-Lab/publication-tags

Add publication tags

Author: JakeWags

layouts/publication.vue

@@ -33,7 +33,6 @@ import { Content, useData } from 'vitepress';
 const { frontmatter } = useData();
 
 function getAuthorsList() {
-  console.log(frontmatter.authors)
   return frontmatter.authors
 }
 </script>

pages/people.md

@@ -14,6 +14,7 @@ const members = ref({
   researchers: [],
   phdStudents: [],
   msStudents: [],
+  undergradStudents: [],
   staff: [],
   alumni: []
 })
@@ -77,6 +78,13 @@ onMounted(async () => {
     </template>
   </VPTeamPageSection>
 
+  <VPTeamPageSection v-if="members.undergradStudents.length">
+      <template #title>Undergrad Students</template>
+    <template #members>
+      <VPTeamMembers :members="members.msStudents" size="small" />
+    </template>
+  </VPTeamPageSection>
+
   <VPTeamPageSection v-if="members.staff.length">
     <template #title>Staff</template>
     <template #members>

pages/publications.md

@@ -10,7 +10,7 @@ const SORT_OPTIONS = {
   ascending: false  // boolean for ascending/descending order, true = ascending
 }
 
-const publications = ref([])
+const publications = ref([]);
 
 const sorting = ref({
   sort: "author",
@@ -22,22 +22,46 @@ const previousSort = ref("author")
 const search = ref("")
 const searchOpen = ref(false)
 
+const selectedTags = ref(new Set([]));
+const tagsOpen = ref(false);
+
 // helper
 function sortByAuthor(a, b, order) {
   const aFirstAuthor = a.authors.split(',')[0]
   const bFirstAuthor = b.authors.split(',')[0]
   const aLastName = aFirstAuthor.split(' ').pop()
   const bLastName = bFirstAuthor.split(' ').pop()
-  return aLastName.localeCompare(bLastName) * order
+  return aLastName.localeCompare(bLastName) * order;
 }
 
+const tags = computed(() => {
+  const t = new Set([]);
+  // get every unique tag from publications.value
+  publications.value.forEach((p) => {
+    if (p.tags) {
+      // for every tag within the publication, add it to the Set object
+      p.tags.forEach((tag) => t.add(tag));
+    }
+  });
+
+  return t;
+});
+
 const sortedPublications = computed(() => {
   // filter search string first
   let filteredPubs = [...publications.value]
   if (search.value !== "") {
     filteredPubs = filteredPubs.filter((p) => p.title.toLowerCase().includes(search.value.toLowerCase()))
   }
 
+  // filter by tags
+  if (selectedTags.value.length > 0) {
+    filteredPubs = filteredPubs.filter((p) => {
+      if (!p.tags) return false
+      return [...selectedTags.value].every(tag => p.tags.includes(tag))
+    });
+  }
+
   return filteredPubs.sort((a, b) => {
     const sortKey = sorting.value.sort
     const order = sorting.value.ascending ? -1 : 1
@@ -74,8 +98,20 @@ function handleSortToggle(v) {
   }
 }
 
+function handleTagSelect(tag) {
+  if (selectedTags.value.has(tag)) {
+    selectedTags.value.delete(tag);
+  } else {
+    selectedTags.value.add(tag);
+  }
+}
+
 function openSearchBar() {
-  searchOpen.value = true
+  searchOpen.value = true;
+}
+
+function openTagsMenu() {
+  tagsOpen.value = true;
 }
 
 onMounted(async () => {
@@ -125,6 +161,21 @@ onMounted(async () => {
   height: 16px; /* Height of the icon */
   display: inline-block;
 }
+
+.tags {
+  padding: 5px;
+  max-width: 250px;
+}
+
+.tag {
+  width: fit-content;
+}
+
+.v-chip--selected {
+  background: var(--vp-c-brand-1);
+  color: white;
+}
+
 </style>
 <span></span>
 <v-row
@@ -160,26 +211,45 @@ onMounted(async () => {
       </v-icon>
       <span v-else class="v-icon-placeholder"></span>
     </v-btn>
-      <v-menu 
-        :close-on-content-click="false"
-        location="bottom"
-      >
-        <template v-slot:activator="{ props }">
-          <v-btn v-bind="props" icon="mdi-magnify" @click="() => {
-            sorting.sort = previousSort  // reset sorting to previous to ignore the click action
-            openSearchBar()
-          }">
-          </v-btn>
-        </template>
-        <v-card min-width="300">
-          <v-text-field
-            v-model="search"
-            hide-details
-            label="Search"
-          >
-          </v-text-field>
-        </v-card>
-      </v-menu>
+    <v-menu 
+      :close-on-content-click="false"
+      location="bottom"
+    >
+      <template v-slot:activator="{ props }">
+        <v-btn v-bind="props" icon="mdi-tag-outline" @click="() => {
+          sorting.sort = previousSort  // reset sorting to previous to ignore the click action
+          openTagsMenu()
+        }">
+        </v-btn>
+      </template>
+      <v-card class="tags">
+      <v-chip-group v-model="selectedTags" column multiple>
+        <v-chip v-for="tag in tags" :key="tag" class="tag" :value="tag">
+          {{tag}}
+        </v-chip>
+      </v-chip-group>
+      </v-card>
+    </v-menu>
+    <v-menu 
+      :close-on-content-click="false"
+      location="bottom"
+    >
+      <template v-slot:activator="{ props }">
+        <v-btn v-bind="props" icon="mdi-magnify" @click="() => {
+          sorting.sort = previousSort  // reset sorting to previous to ignore the click action
+          openSearchBar()
+        }">
+        </v-btn>
+      </template>
+      <v-card min-width="300">
+        <v-text-field
+          v-model="search"
+          hide-details
+          label="Search"
+        >
+        </v-text-field>
+      </v-card>
+    </v-menu>
   </v-btn-toggle>
 </v-row>
 

pages/publications/2020_uncertain_deepssm.md

@@ -4,6 +4,7 @@ title: "Uncertain-DeepSSM: From Images to Probabilistic Shape Models"
 authors: "Jadie Adams, Riddhish Bhalodia, Shireen Elhabian"
 conference: "Shape in Medical Imaging (ShapeMI) at MICCAI"
 year: "2020"
+tags: ["Deep Learning", "DeepSSM", "SSM"]
 links:
   archive: "https://arxiv.org/abs/2007.06516"
 image:

pages/publications/2021_benchmarking.md

@@ -9,6 +9,7 @@ links:
 image:
   src: "2021_benchmarking.jpg"
   alt: Benchmarking FrameWork
+tags: ["SSM"]
 ---
 
 # Benchmarking Off-the-shelf Statistical Shape Modeling Tools in Clinical Applications

pages/publications/2022_rvtr.md

@@ -10,6 +10,7 @@ links:
 image:
   src: "2022_rvtr.jpg"
   alt: Results Highlight
+tags: ["SSM"]
 ---
 
 # All Roads Lead to Rome: Diverse Etiologies of Tricuspid Regurgitation Create a Predictable Constellation of Right Ventricular Shape Changes

pages/publications/2022_sharedboundary.md

@@ -9,6 +9,7 @@ links:
 image:
   src: "2022_stacom_shared.jpg"
   alt: Results Highlight
+tags: ["SSM", "Anatomy"]
 ---
 
 # Statistical Shape Modeling of Biventricular Anatomy with Shared Boundaries

pages/publications/2022_spatiotemporal_ssm.md

@@ -9,6 +9,7 @@ links:
 image:
   src: "2022_spatiotemporal_ssm.png"
   alt: Results Highlight
+tags: ["SSM", "Anatomy", "Cardiac"]
 ---
 
 # Spatiotemporal Cardiac Statistical Shape Modeling: A Data-Driven Approach

pages/publications/2022_vib_deepssm.md

@@ -10,6 +10,7 @@ links:
 image:
   src: "2022_vib_deepssm.png"
   alt: Results Highlight
+tags: ["DeepSSM", "SSM"]
 ---
 
 # From Images to Probabilistic Anatomical Shapes: A Deep Variational Bottleneck Approach

pages/publications/2023_ADASSM.md

@@ -9,6 +9,7 @@ links:
 image:
   src: "2023_ADASSM.png"
   alt: Results Highlight
+tags: ["SSM"]
 ---
 
 # ADASSM: Adversarial Data Augmentation in Statistical Shape Models From Images

pages/publications/2023_Automated_Annotation_pathology.md

@@ -9,6 +9,7 @@ links:
 image:
   src: "2023_Automated_Annotation_pathology.png"
   alt: Automated Annotation
+tags: ['Deep Learning', 'Image Processing']
 ---
 
 # End to End processing Pipeline for Automated Annotation using Immunohistochemistry.

pages/publications/2023_SCGAN_virtual_staining.md

@@ -9,6 +9,7 @@ links:
 image:
   src: "2023_SCGAN_virtual_staining.png"
   alt: Structural CycleGAN
+tags: ['Deep Learning']
 ---
 
 # Propose a new architecture for Virtual Staining regularizing the learning via structural consistency.

pages/publications/2023_benchmarking_pathology_pretraining.md

@@ -10,6 +10,7 @@ links:
 image:
   src: "2023_benchmarking_pathology_pretraining.png"
   alt: Benchmarking Semantic Segmentation
+tags: ['Image Processing', 'Segmentation']
 ---
 
 # Benchmarking Whether Domain Specific pretraining helps in better gland and cell segmentation in histopathology

pages/publications/2023_benchmarking_segmentation.md

@@ -9,6 +9,7 @@ links:
 image:
   src: "2023_benchmarking_segmentation.png"
   alt: Results Highlight
+tags: ['Segmentation']
 ---
 
 # Benchmarking Scalable Epistemic Uncertainty Quantification in Organ Segmentation

pages/publications/2023_bvib_deepssm.md

@@ -10,6 +10,7 @@ links:
 image:
   src: "2023_bvib_deepssm.png"
   alt: Results Highlight
+tags: ['DeepSSM', 'SSM']
 ---
 
 # Fully Bayesian VIB DeepSSM

pages/publications/2023_can_pointclouds.md

@@ -10,6 +10,7 @@ links:
 image:
   src: "2023_can_pointclouds.png"
   alt: Results Highlight
+tags: ['SSM', 'Anatomy']
 ---
 
 # Can point cloud networks learn statistical shape models of anatomies?

pages/publications/2023_frontiers_sharedboundary.md

@@ -9,6 +9,7 @@ links:
 image:
   src: "2023_frontiers_shared.jpg"
   alt: Results Highlight
+tags: ['SSM', 'Anatomy']
 ---
 
 # Statistical Shape Modeling of Multi-Organ Anatomies with Shared Boundaries: A Data-Driven Approach

pages/publications/2023_frontiers_spatiotemporal_ssm.md

@@ -9,6 +9,7 @@ links:
 image:
   src: "2023_frontiers_spatiotemporal_ssm.jpg"
   alt: Results Highlight
+tags: ['SSM']
 ---
 
 # Learning Spatiotemporal Statistical Shape Models for Non-Linear Dynamic Anatomies

pages/publications/2023_mesh2ssm.md

@@ -10,6 +10,7 @@ links:
 image:
   src: "2023_mesh2ssm.png"
   alt: Mesh2SSM Model
+tags: ['Deep Learning', 'SSM']
 ---
 
 # Mesh2SSM: From Surface Meshes to Statistical Shape Models of Anatomy

pages/publications/2024_MASSM.md

@@ -9,6 +9,7 @@ links:
 image:
   src: "2024_MASSM.png"
   alt: Automated Annotation
+tags: ['Deep learning', 'SSM']
 ---
 
 # A method for multi-anatomy SSM directly from Images.

pages/publications/2024_SlicePropUQ.md

@@ -6,6 +6,7 @@ conference: "International Conference on Medical Image Computing and Computer-As
 year: "2024"
 links:
   publisher: "https://link.springer.com/chapter/10.1007/978-3-031-72117-5_26"
+tags: ['Segmentation', 'Image Processing']
 ---
 
 # Uncertainty Quantification for Slice Propagation Models

pages/publications/2024_UDA_Density_Matching.md

@@ -9,6 +9,7 @@ links:
 image:
   src: "2024_UDA_Density_Matching.png"
   alt: UDA Density Matching
+tags: ['Deep Learning', 'Segmentation']
 ---
 
 # Method for Unsupervised Domain Adaptation using Target Density Matching

pages/publications/2024_point2ssm.md

@@ -10,6 +10,7 @@ links:
 image:
   src: "2024_point2ssm.png"
   alt: Results Highlight
+tags: ['Deep Learning', 'SSM']
 ---
 
 # Point2SSM: Learning Morphological Variations of Anatomies from Point Cloud

pages/publications/2024_scorp.md

@@ -10,6 +10,7 @@ links:
 image:
   src: "2024_scorp.jpg"
   alt: Results Highlight
+tags: ['Image Processing', 'Deep Learning']
 ---
 
 # SCorP: Statistics-Informed Dense Correspondence Prediction Directly from Unsegmented Medical Images

pages/publications/2024_spicorrnet.md

@@ -9,6 +9,7 @@ links:
 image:
   src: "2024_spicorrnet.jpg"
   alt: Results Highlight
+tags: ['SSM', 'Deep Learning']
 ---
 
 # Probabilistic 3D Correspondence Prediction from Sparse Unsegmented Images

pages/publications/2024_weaklydeepssm.md

@@ -9,6 +9,7 @@ links:
 image:
   src: "2024_weaklydeepssm.png"
   alt: Results Highlight
+tags: ['SSM', 'Deep Learning']
 ---
 
 # Weakly Supervised Bayesian Shape Modeling from Medical Images

pages/publications/2025_EfficientMorph.md

@@ -10,6 +10,7 @@ links:
 image:
   src: "2025_EfficientMorph.png"
   alt: Efficient Architectures
+tags: ['Image Processing', 'Image Registration']
 ---
 
 # A parameter efficient model for transformer based 3D registation