From 0cb63a8e3b75634176a1f5ae4d8885549fe448d8 Mon Sep 17 00:00:00 2001
From: alan-wu <alan.wu@auckland.ac.nz>
Date: Wed, 4 Feb 2026 16:22:03 +1300
Subject: [PATCH 1/3] Remove biolucida images and segmentation.

---
 src/components/BadgesGroup.vue     |  3 +-
 src/components/DatasetCard.vue     | 30 ----------
 src/components/DatasetExplorer.vue |  1 -
 src/components/ImageGallery.vue    | 93 ------------------------------
 4 files changed, 1 insertion(+), 126 deletions(-)

diff --git a/src/components/BadgesGroup.vue b/src/components/BadgesGroup.vue
index e198ad59..e43e4cc6 100644
--- a/src/components/BadgesGroup.vue
+++ b/src/components/BadgesGroup.vue
@@ -88,7 +88,6 @@ export default {
         this.addToCategories(this.entry.flatmaps, 'Flatmaps')
         this.addToCategories(this.entry.plots, 'Plots')
         this.addToCategories(this.entry.scaffolds, 'Scaffolds')
-        this.addToCategories(this.entry.segmentation, 'Segmentations')
         this.addSimulationsToCategories(this.entry.simulation)
         /** disable the following
         this.addToCategories(this.entry.images, 'Images');
@@ -117,7 +116,7 @@ export default {
       color: #fff!important;
     }
   }
-  
+
   .tag-button + .tag-button {
     margin-left: 0!important;
   }
diff --git a/src/components/DatasetCard.vue b/src/components/DatasetCard.vue
index a3205e57..370ee4ae 100644
--- a/src/components/DatasetCard.vue
+++ b/src/components/DatasetCard.vue
@@ -12,7 +12,6 @@
             :envVars="envVars"
             :label="label"
             :datasetThumbnail="thumbnail"
-            :dataset-biolucida="biolucidaData"
             :category="currentCategory"
             @card-clicked="galleryClicked"
             @datalink-clicked="galleryDatalinkClicked"
@@ -42,7 +41,6 @@
           <div class="badges-container">
             <BadgesGroup
               :entry="entry"
-              :dataset-biolucida="biolucidaData"
               @categoryChanged="categoryChanged"
             />
           </div>
@@ -60,7 +58,6 @@
 <script>
 /* eslint-disable no-alert, no-console */
 import { View as ElIconView } from '@element-plus/icons-vue'
-import { Base64  } from 'js-base64';
 import BadgesGroup from './BadgesGroup.vue'
 import {
   ElButton as Button,
@@ -109,7 +106,6 @@ export default {
       loading: true,
       version: 1,
       lastDoi: undefined,
-      biolucidaData: undefined,
       currentCategory: 'All',
       copyContent: '',
     }
@@ -237,7 +233,6 @@ export default {
             this.discoverId = data.id
             this.version = data.version
             this.dataLocation = `https://sparc.science/datasets/${data.id}?type=dataset`
-            this.getBiolucidaInfo()
             this.loading = false
             this.updateCopyContent();
           })
@@ -252,31 +247,6 @@ export default {
     lastName: function (fullName) {
       return fullName.split(',')[0]
     },
-    getBiolucidaInfo: function () {
-      const dataset_images = [];
-      const biolucida2DItems = 'biolucida-2d' in this.entry ? this.entry['biolucida-2d'] :[];
-      const biolucida3DItems = 'biolucida-3d' in this.entry ? this.entry['biolucida-3d'] :[];
-      // We use information from SciCrunch to create the sharelink
-      biolucida2DItems.concat(biolucida3DItems).forEach((bObject) => {
-        const image_id = bObject.biolucida?.identifier;
-        if (image_id) {
-          const sourcepkg_id = 'identifier' in bObject ? bObject['identifier'] : "";
-          // The encoded string is in the following format -
-          // ${image_id}-col-${collection_id}, collection id can be any valid collection id
-          // and 260 is used for now.
-          const code = encodeURIComponent(Base64.encode(`${image_id}-col-260`));
-          const share_link = `https://sparc.biolucida.net/image?c=${code}`
-          dataset_images.push({
-            share_link,
-            image_id,
-            sourcepkg_id,
-          });
-        }
-      });
-      if (dataset_images.length > 0) {
-        this.biolucidaData = { dataset_images };
-      }
-    },
     updateCopyContent: function () {
       const contentArray = [];
 
diff --git a/src/components/DatasetExplorer.vue b/src/components/DatasetExplorer.vue
index d4783989..a12ba80c 100644
--- a/src/components/DatasetExplorer.vue
+++ b/src/components/DatasetExplorer.vue
@@ -499,7 +499,6 @@ export default {
             element['abi-contextual-information'].length > 0
               ? element['abi-contextual-information']
               : undefined,
-          segmentation: element['mbf-segmentation'],
           //omex format will be the preferred mimetype
           simulation: element['abi-simulation-omex-file'] ? element['abi-simulation-omex-file'] : element['abi-simulation-file'],
           flatmaps: element['abi-flatmap-file'],
diff --git a/src/components/ImageGallery.vue b/src/components/ImageGallery.vue
index 5f9ac867..cc8235be 100644
--- a/src/components/ImageGallery.vue
+++ b/src/components/ImageGallery.vue
@@ -40,12 +40,6 @@ export default {
   components: { Gallery },
   mixins: [GalleryHelper, S3Bucket],
   props: {
-    datasetBiolucida: {
-      type: Object,
-      default: () => {
-        return {}
-      },
-    },
     envVars: {
       type: Object,
       default: () => {},
@@ -89,13 +83,10 @@ export default {
       ro: null,
       maxWidth: 3,
       items: {
-        //Use the Images instead for Biolucida Images
-        //"Biolucida Images": [],
         Dataset: [],
         Flatmaps:[],
         Images: [],
         Scaffolds: [],
-        Segmentations: [],
         Simulations: [],
         Videos: [],
         Plots: [],
@@ -128,7 +119,6 @@ export default {
       this.createScaffoldItems()
       this.createSimulationItems()
       this.createPlotItems()
-      this.createSegmentationItems()
       /* Disable these two
       this.createImageItems();
       this.createVideoItems();
@@ -324,47 +314,6 @@ export default {
         })
       }
     },
-    createSegmentationItems: function () {
-      if (this.entry.segmentation) {
-        this.entry.segmentation.forEach((segmentation) => {
-          const id = segmentation.id
-          let filePath = segmentation.dataset.path
-          filePath = filePath.replaceAll(' ', '_')
-          filePath = filePath.replaceAll(',', '_')
-          const prefix = this.envVars.NL_LINK_PREFIX
-          const resource = {
-            share_link: `${prefix}/dataviewer?datasetId=${this.datasetId}&version=${this.datasetVersion}&path=files/${filePath}`,
-          }
-          let action = {
-            label: capitalise(this.label),
-            resource: resource,
-            datasetId: this.datasetId,
-            s3uri: this.entry.s3uri,
-            title: 'View segmentation',
-            type: 'Segmentation',
-          }
-          const thumbnailURL = this.getSegmentationThumbnailURL(
-            this.envVars.API_LOCATION,
-            {
-              id,
-              datasetId: this.datasetId,
-              datasetVersion: this.datasetVersion,
-              segmentationFilePath: filePath,
-              s3Bucket: this.s3Bucket,
-            }
-          )
-          this.items['Segmentations'].push({
-            id,
-            title: baseName(filePath),
-            type: 'Segmentation',
-            thumbnail: thumbnailURL,
-            userData: action,
-            hideType: true,
-            mimetype: 'image/png',
-          })
-        })
-      }
-    },
     createSimulationItems: function () {
       if (this.entry.simulation) {
         this.entry.simulation.forEach((simulation) => {
@@ -496,48 +445,6 @@ export default {
     galleryItems: function () {
       this.resetIndex = false
     },
-    datasetBiolucida: {
-      deep: true,
-      immediate: true,
-      handler: function (biolucidaData) {
-        let items = []
-        if ('dataset_images' in biolucidaData) {
-          items.push(
-            ...Array.from(biolucidaData.dataset_images, (dataset_image) => {
-              const thumbnailURL = this.getThumbnailURLFromBiolucida(
-                this.envVars.API_LOCATION,
-                {
-                  id: dataset_image.image_id,
-                }
-              )
-              const resource = {
-                share_link: dataset_image.share_link,
-                id: dataset_image.image_id,
-                itemId: dataset_image.sourcepkg_id,
-              }
-              let action = {
-                label: capitalise(this.label),
-                resource: resource,
-                datasetId: this.datasetId,
-                title: 'View image',
-                name: capitalise(this.label),
-                type: 'Biolucida',
-              }
-              return {
-                id: dataset_image.image_id,
-                title: `Image`,
-                type: 'Image',
-                thumbnail: thumbnailURL,
-                userData: action,
-                mimetype: 'image/png',
-                hideType: true,
-              }
-            })
-          )
-        }
-        this.items['Images'] = items
-      },
-    },
   },
   mounted() {
     this.ro = new ResizeObserver(this.onResize).observe(this.$el)

From 4fe0b02e161a2e8f7cd6097741ae437437d5b350 Mon Sep 17 00:00:00 2001
From: alan-wu <alan.wu@auckland.ac.nz>
Date: Thu, 5 Feb 2026 11:11:31 +1300
Subject: [PATCH 2/3] Remove an unused environment variable.

---
 src/App.vue                | 1 -
 src/components/SideBar.vue | 5 ++---
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/App.vue b/src/App.vue
index 4d2db5d9..3299be0d 100644
--- a/src/App.vue
+++ b/src/App.vue
@@ -134,7 +134,6 @@ export default {
         ALGOLIA_INDEX: import.meta.env.VITE_APP_ALGOLIA_INDEX,
         PENNSIEVE_API_LOCATION: import.meta.env.VITE_APP_PENNSIEVE_API_LOCATION,
         BL_SERVER_URL: import.meta.env.VITE_APP_BL_SERVER_URL,
-        NL_LINK_PREFIX: import.meta.env.VITE_APP_NL_LINK_PREFIX,
         ROOT_URL: import.meta.env.VITE_APP_ROOT_URL,
         FLATMAPAPI_LOCATION: import.meta.env.VITE_FLATMAPAPI_LOCATION,
       },
diff --git a/src/components/SideBar.vue b/src/components/SideBar.vue
index b27cde12..377bd0bc 100644
--- a/src/components/SideBar.vue
+++ b/src/components/SideBar.vue
@@ -129,9 +129,8 @@ export default {
     },
     /**
      * The environment variables object with
-     * `API_LOCATION`, `ALGOLIA_KEY`, `ALGOLIA_ID`,
-     * `ALGOLIA_INDEX`, `PENNSIEVE_API_LOCATION`, `BL_SERVER_URL`,
-     * `NL_LINK_PREFIX`, `ROOT_URL`
+     * `API_LOCATION`, `ALGOLIA_KEY`, `ALGOLIA_ID`, `ALGOLIA_INDEX`,
+     * `PENNSIEVE_API_LOCATION`, `BL_SERVER_URL`, `ROOT_URL`
      */
     envVars: {
       type: Object,

From 2723fca8f11855d9d9012a0a40a32005d0a33312 Mon Sep 17 00:00:00 2001
From: akhuoa <aung.kyaw.hein@auckland.ac.nz>
Date: Thu, 5 Feb 2026 11:40:36 +1300
Subject: [PATCH 3/3] Remove biolucida

---
 README.md                      |  2 --
 src/components/BadgesGroup.vue | 15 ---------------
 2 files changed, 17 deletions(-)

diff --git a/README.md b/README.md
index 98c9e7e7..e4c7bf9f 100644
--- a/README.md
+++ b/README.md
@@ -92,8 +92,6 @@ https://github.com/nih-sparc/sparc-api/blob/f3444a32964f5340e0ee1f10a08a05839620
 
 ```
 ADDITIONAL_LINKS = 'additionalLinks'
-BIOLUCIDA_2D = 'biolucida-2d'
-BIOLUCIDA_3D = 'biolucida-3d'
 COMMON_IMAGES = 'common-images'
 CONTEXT_FILE = 'abi-context-file'
 CSV = 'csv'
diff --git a/src/components/BadgesGroup.vue b/src/components/BadgesGroup.vue
index e43e4cc6..cf55e6d1 100644
--- a/src/components/BadgesGroup.vue
+++ b/src/components/BadgesGroup.vue
@@ -32,12 +32,6 @@ export default {
         return []
       },
     },
-    datasetBiolucida: {
-      type: Object,
-      default: () => {
-        return {}
-      },
-    },
     entry: {
       type: Object,
       default: () => {
@@ -72,15 +66,6 @@ export default {
     },
   },
   watch: {
-    datasetBiolucida: {
-      deep: true,
-      immediate: true,
-      handler: function (biolucidaData) {
-        if ('dataset_images' in biolucidaData) {
-          this.addToCategories(biolucidaData['dataset_images'], 'Images')
-        }
-      },
-    },
     entry: {
       deep: true,
       immediate: true,