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Remove biolucida images and segmentation. #203

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0cb63a8
Remove biolucida images and segmentation.
alan-wu Feb 4, 2026
4fe0b02
Remove an unused environment variable.
alan-wu Feb 4, 2026
2723fca
Remove biolucida
akhuoa Feb 4, 2026
d1cf914
Merge pull request #14 from akhuoa/remove-biolucida
alan-wu Feb 4, 2026
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2 changes: 0 additions & 2 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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'
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1 change: 0 additions & 1 deletion src/App.vue
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Expand Up @@ -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,
},
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18 changes: 1 addition & 17 deletions src/components/BadgesGroup.vue
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Expand Up @@ -32,12 +32,6 @@ export default {
return []
},
},
datasetBiolucida: {
type: Object,
default: () => {
return {}
},
},
entry: {
type: Object,
default: () => {
Expand Down Expand Up @@ -72,23 +66,13 @@ 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,
handler: function () {
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');
Expand Down Expand Up @@ -117,7 +101,7 @@ export default {
color: #fff!important;
}
}

.tag-button + .tag-button {
margin-left: 0!important;
}
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30 changes: 0 additions & 30 deletions src/components/DatasetCard.vue
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Expand Up @@ -12,7 +12,6 @@
:envVars="envVars"
:label="label"
:datasetThumbnail="thumbnail"
:dataset-biolucida="biolucidaData"
:category="currentCategory"
@card-clicked="galleryClicked"
@datalink-clicked="galleryDatalinkClicked"
Expand Down Expand Up @@ -42,7 +41,6 @@
<div class="badges-container">
<BadgesGroup
:entry="entry"
:dataset-biolucida="biolucidaData"
@categoryChanged="categoryChanged"
/>
</div>
Expand All @@ -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,
Expand Down Expand Up @@ -109,7 +106,6 @@ export default {
loading: true,
version: 1,
lastDoi: undefined,
biolucidaData: undefined,
currentCategory: 'All',
copyContent: '',
}
Expand Down Expand Up @@ -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();
})
Expand All @@ -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 = [];

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1 change: 0 additions & 1 deletion src/components/DatasetExplorer.vue
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Expand Up @@ -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'],
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93 changes: 0 additions & 93 deletions src/components/ImageGallery.vue
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Expand Up @@ -40,12 +40,6 @@ export default {
components: { Gallery },
mixins: [GalleryHelper, S3Bucket],
props: {
datasetBiolucida: {
type: Object,
default: () => {
return {}
},
},
envVars: {
type: Object,
default: () => {},
Expand Down Expand Up @@ -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: [],
Expand Down Expand Up @@ -128,7 +119,6 @@ export default {
this.createScaffoldItems()
this.createSimulationItems()
this.createPlotItems()
this.createSegmentationItems()
/* Disable these two
this.createImageItems();
this.createVideoItems();
Expand Down Expand Up @@ -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) => {
Expand Down Expand Up @@ -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)
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5 changes: 2 additions & 3 deletions src/components/SideBar.vue
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Expand Up @@ -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,
Expand Down