Merge pull request #115 from aeisenbarth/spacem

Add SpaceM datasets
scverse · Jan 20, 2025 · 0a2a1c1 · 0a2a1c1
2 parents 729ccb8 + 208395e
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diff --git a/_static/img/spacem_helanih3t3.png b/_static/img/spacem_helanih3t3.png
diff --git a/datasets/README.md b/datasets/README.md
@@ -15,6 +15,8 @@ If you want to convert additional datasets check out the scripts available in th
 | MIBI-TOF                                  | Colorectal carcinoma [^6]                                 |     25 MB | mibitof                        | [.zarr.zip](https://s3.embl.de/spatialdata/spatialdata-sandbox/mibitof.zip)                     | [S3](https://s3.embl.de/spatialdata/spatialdata-sandbox/mibitof.zarr/)                     | CC BY 4.0 DEED    |
 | Imaging Mass Cytometry (Steinbock output) | 4 different cancers (SCCHN, BCC, NSCLC, CRC) [^7][^8][^9] |    820 MB | steinbock_io                   | [.zarr.zip](https://s3.embl.de/spatialdata/spatialdata-sandbox/steinbock_io.zip)                | [S3](https://s3.embl.de/spatialdata/spatialdata-sandbox/steinbock_io.zarr/)                | CC BY 4.0 DEED    |
 | Molecular Cartography (SPArrOW output)    | Mouse Liver [^10][^11]                                    |     70 MB | MouseLiver                     | [.zarr.zip](https://s3.embl.de/spatialdata/spatialdata-sandbox/mouse_liver.zip)                 | [S3](https://s3.embl.de/spatialdata/spatialdata-sandbox/mouse_liver.zarr)                  | CC BY 4.0 DEED    |
+| SpaceM                                    | T cells [^12]                                             |    116 MB | spacem_scseahorse1             | [.zarr.zip](https://s3.embl.de/spatialdata/raw_data/20220121_ScSeahorse1.zip)                   | NA                                                                                         | CC BY 4.0 DEED    |
+| SpaceM                                    | Hepa and NIH3T3 cells [^13]                               |     59 MB | spacem_hepanih3t3              | [.zarr.zip](https://s3.embl.de/spatialdata/raw_data/20221014_HeLaNIH3T3.zip)                    | NA                                                                                         | CC BY 4.0 DEED    |
 
 For the first 3 datasets, we also provide a version of them in which they are all aligned in a common coordinate system, and where we added the cell-type information, as described in our paper, to annotate the Xenium cells.
 | Technology | Sample | File Size | Filename (spatialdata-sandbox) | download data | work with data remotely (**see note below**) | license |
@@ -66,3 +68,7 @@ If you use the datasets please cite the original sources and double-check their
 [^10]: Guilliams, Martin, et al. "Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches." Cell 185.2 (2022) doi:10.1016/j.cell2021.12.018
 
 [^11]: Pollaris, Lotte, et al. "SPArrOW: a flexible, interactive and scalable pipeline for spatial transcriptomics analysis." bioRxiv (2024) doi:10.1101/2024.07.04.601829
+
+[^12]: See https://github.com/giovp/spatialdata-sandbox/blob/main/spacem_scseahorse1/README.md
+
+[^13]: See https://github.com/giovp/spatialdata-sandbox/blob/main/spacem_helanih3t3/README.md
diff --git a/notebooks.md b/notebooks.md
@@ -240,6 +240,17 @@ Many different technologies can be visualised out-of-the-box. See below for a co
 
                 notebooks/examples/technology_xenium.ipynb
 
+    .. grid-item::
+
+        .. container:: custom-card
+
+            .. image:: _static/img/spacem_helanih3t3.png
+                :target: notebooks/examples/technology_spacem.html
+
+            .. toctree::
+                :maxdepth: 1
+
+                notebooks/examples/technology_spacem.ipynb
 
 ```
 

diff --git a/notebooks/examples/alignment_using_landmarks.ipynb b/notebooks/examples/alignment_using_landmarks.ipynb
@@ -181,13 +181,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "if 'visium_landmarks' in visium_sdata:\n",
+    "if \"visium_landmarks\" in visium_sdata:\n",
     "    visium_sdata.delete_element_from_disk(\"visium_landmarks\")\n",
-    "    del visium_sdata['visium_landmarks']\n",
+    "    del visium_sdata[\"visium_landmarks\"]\n",
     "\n",
-    "if 'xenium_landmarks' in xenium_sdata:\n",
+    "if \"xenium_landmarks\" in xenium_sdata:\n",
     "    xenium_sdata.delete_element_from_disk(\"xenium_landmarks\")\n",
-    "    del xenium_sdata['xenium_landmarks']"
+    "    del xenium_sdata[\"xenium_landmarks\"]"
    ]
   },
   {

diff --git a/notebooks/examples/technology_spacem.ipynb b/notebooks/examples/technology_spacem.ipynb