Add new template 'lightweight-thymus' with fixes

src/tags.json

@@ -13,5 +13,8 @@
   "hra": "Human Reference Atlas data",
   "sc": "Single cell analysis",
   "R": "Template written in R",
-  "zarr": "Using zarr file format"
+  "zarr": "Using zarr file format",
+  "cellpose": "Using cellpose for cellular segmentation",
+  "imc": "Imaging Mass Cytometry data",
+  "czi": "Using CZI data"
 }

src/user_templates_api/templates/jupyter_lab/templates/lightweight-thymus/README.md

@@ -0,0 +1,7 @@
+Last edited: Nov 17, 2024
+Works with UUIDs: ['43213991a54ce196d406707ffe2e86bd', 
+    '822c9163d3be9b427dd0830f69a12305', 
+    'd4e9ec618924a8d43cfe1e67c38c1447', 
+    '37d06bb991afa2beb7b9460e746247ad', 
+    '9a6403bb0423e62950926a7d4fdab45b',]
+

src/user_templates_api/templates/jupyter_lab/templates/lightweight-thymus/metadata.json

@@ -0,0 +1,39 @@
+{
+  "title": "Lightweight thymus feature analysis using CODEX [CytoKit+SPRM]",
+  "description": "Parameterize cellpose3 to segment and quantify CODEX protein signal in thymus Hassall's corpuscles. Compare with (i) CODEX CytoKit+SPRM, (ii) 2D IMC protein, and (iii) CZI Science cellxgene single-cell RNA.",
+  "tags": [
+    "cellpose",    
+    "codex",
+    "zarr",
+    "anndata",
+    "imc",
+    "czi"
+  ], 
+  "is_multi_dataset_template": true,
+  "template_format": "jinja",
+  "examples": [
+    {
+      "title": "Lightweight thymus feature analysis using CODEX [CytoKit+SPRM]",
+      "description": "Parameterize cellpose3 to segment and quantify CODEX protein signal in thymus Hassall's corpuscles. Compare with (i) CODEX CytoKit+SPRM, (ii) 2D IMC protein, and (iii) CZI Science cellxgene single-cell RNA.",
+      "assay_display_name": ["CODEX [CytoKit+SPRM]"],
+      "datasets": [
+        "43213991a54ce196d406707ffe2e86bd",
+        "822c9163d3be9b427dd0830f69a12305",
+        "d4e9ec618924a8d43cfe1e67c38c1447",
+        "37d06bb991afa2beb7b9460e746247ad",
+        "9a6403bb0423e62950926a7d4fdab45b"
+      ]
+    }
+  ],
+  "contributors": [
+    {
+      "name": "Soo Hee Lee",
+      "affiliation": "10x Genomics",
+      "orcid": "",
+      "github": "sooheelee",
+      "email": ""
+    }
+  ],
+  "is_hidden": false,
+  "last_modified_unix_timestamp": 1739368453
+}

src/user_templates_api/templates/jupyter_lab/templates/lightweight-thymus/render.py

@@ -0,0 +1,6 @@
+from user_templates_api.templates.jupyter_lab.render import JupyterLabRender
+
+
+class JupyterLabExampleJinjaRender(JupyterLabRender):
+    def __init__(self):
+        pass