Merge pull request #1484 from FZJ-INM1-BDA/staging

v2.14.17

Author: xgui3783

.prepare_release.mjs

@@ -93,7 +93,9 @@ async function updateCodemeta(version){
 
   const date = new Date()
   const YYYY = date.getFullYear().toString()
-  const MM = date.getMonth().toString().padStart(2, "0")
+  // getMonth returns index 0 month...
+  // see https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Date/getMonth
+  const MM = (date.getMonth() + 1).toString().padStart(2, "0")
   const DD = date.getDate().toString()
 
   codemetaContent["dateModified"] = `${YYYY}-${MM}-${DD}`

codemeta.json

@@ -57,7 +57,7 @@
     ],
     "codeRepository": "git+https://github.com/fzj-inm1-bda/siibra-explorer.git",
     "dateCreated": "2024-08-28",
-    "dateModified": "2025-01-28",
+    "dateModified": "2025-03-18",
     "datePublished": "2019-04-26",
     "description": "`siibra-explorer` is a browser based 3D viewer for exploring brain atlases that cover different spatial resolutions and modalities. It is built around an interactive 3D view of the brain displaying a unique selection of detailed templates and parcellation maps for the human, macaque, rat or mouse brain, including BigBrain as a microscopic resolution human brain model at its full resolution of 20 micrometers. ",
     "license": "https://spdx.org/licenses/Apache-2.0",
@@ -66,9 +66,9 @@
         "python 3",
         "typescript"
     ],
-    "schema:releaseNotes": "# v2.14.16\n\n## Feature\n\n- allow position of substrate to be customized (#1479)\n- parse template `meta.json` endpoint, and use RBG color map when prompted\n- drag&drop nifti auto clamp & auto set highest value as threshold max\n- (experimental): added support to fetch `.dzi` transform\n- (experimental): added support for zarr(2) as data feature\n\n## Bugfix\n\n- fix issue where repeated request for saneURL yield unstable behavior\n- fix regression where oblique slicing in parcellation with large number of regions causes signficant slow down\n\n## Behind the scene\n\n- added prepare release to package.json script\n- bump ng-layer-tune version, for inclusion of orange colormap\n- use more efficient endpoint to retrieve available maps\n- attempt to parse template theme (dark/light) via `meta.json`\n- parses opacity attribute of volumes overlay volumes via `meta.json`\n",
+    "schema:releaseNotes": "# v2.14.17\n\n## Documentation\n\n- added video tutorial on drag and drop nifti\n- fixed latest release script",
     "runtimePlatform": "docker",
-    "version": "2.14.16",
+    "version": "2.14.17",
     "contIntegration": "https://github.com/FZJ-INM1-BDA/siibra-explorer/actions",
     "codemeta:continuousIntegration": {
         "id": "https://github.com/FZJ-INM1-BDA/siibra-explorer/actions"

docs/.gitignore

@@ -1 +1,2 @@
 autogen_images
+venv

docs/advanced/superimposing_local_files.md

@@ -10,6 +10,12 @@ siibra-explorer experimentally supports overlaying spatial features on top of ex
 
 To start, navigate to the atlas/template/parcellation map of your choice, then drag and drop the file you would like to super impose.
 
+<figure>
+  <video controls="true" allowfullscreen="true">
+    <source src="https://data-proxy.ebrains.eu/api/v1/buckets/interactive-atlas-viewer/videos/20250221-drag-drop-siibra-paper.mp4" type="video/mp4">
+  </video>
+</figure>
+
 ## NIFTI
 
 !!! info

docs/releases/v2.14.17.md

@@ -0,0 +1,6 @@
+# v2.14.17
+
+## Documentation
+
+- added video tutorial on drag and drop nifti
+- fixed latest release script

mkdocs.yml

@@ -45,6 +45,7 @@ nav:
     - Differential gene expression analysis: "advanced/differential_gene_expression_analysis.md"
 
   - Release notes:
+    - v2.14.17: 'releases/v2.14.17.md'
     - v2.14.16: 'releases/v2.14.16.md'
     - v2.14.15: 'releases/v2.14.15.md'
     - v2.14.14: 'releases/v2.14.14.md'

package.json

@@ -1,6 +1,6 @@
 {
   "name": "siibra-explorer",
-  "version": "2.14.16",
+  "version": "2.14.17",
   "description": "siibra-explorer - explore brain atlases. Based on humanbrainproject/nehuba & google/neuroglancer. Built with angular",
   "scripts": {
     "lint": "eslint src --ext .ts",

src/atlasComponents/sapi/translateV3.ts

@@ -31,9 +31,25 @@ function metaFactory(url: string): MetaV1Schema{
         type: "image/1d",
         range: [{
           min: 0.218,
-          max: 0.220
+          max: 0.221
         }]
-      }
+      },
+      bestViewPoints: [{
+        type: "enclosed",
+        points: [{
+          type: "point",
+          value: [-70.677, 0, 62.222]
+        },{
+          type: "point",
+          value: [-70.677, 0, -58.788]
+        },{
+          type: "point",
+          value: [68.533, 0, -58.788]
+        },{
+          type: "point",
+          value: [68.533, 0, 62.222]
+        }]
+      }],
     }
   }
   if (url.includes("tanner")) {