Merge pull request #85 from scverse/fix/download_paths

fix download urls

Author: LucaMarconato

notebooks/examples/densenet.ipynb

@@ -138,11 +138,9 @@
    "id": "01df1f51-29db-4955-8189-42648e5cd95e",
    "metadata": {},
    "source": [
-    "We will need two Zarr files, one for Xenium data and one for Visium data. You can obtain these files by running [this notebook](https://github.com/scverse/spatialdata-notebooks/blob/main/notebooks/paper_reproducibility/xenium_and_visium.ipynb).\n",
+    "You can download the processed Visium and Xenium data (already aligned and Xenium with already the celltype information) from here: [Visium dataset](https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io_aligned.zip), [Xenium dataset](https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep1_io_aligned.zip). In alternative you can obtain the data by running [this analysis notebook](https://github.com/scverse/spatialdata-notebooks/blob/main/notebooks/paper_reproducibility/00_xenium_and_visium.ipynb).\n",
     "\n",
-    "Alternatively, you can download a zipped version of the data from here: [Xenium data](https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep1_io.zip), [Visium data](https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zip). \n",
-    "\n",
-    "If you download the data, please make it discoverable in the paths specified next (you can use symlink to achieve this)."
+    "Please rename the files to `visium_aligned.zarr` and `xenium_aligned.zarr` and place them in the same folder as this notebook (or use symlinks to make the data accessible)."
    ]
   },
   {
@@ -179,14 +177,8 @@
     }
    ],
    "source": [
-    "print(\"current working directory:\", os.getcwd())\n",
-    "SPATIALDATA_SANDBOX_PATH = \"../../../spatialdata-sandbox\"\n",
-    "assert os.path.isdir(\n",
-    "    SPATIALDATA_SANDBOX_PATH\n",
-    "), f\"{SPATIALDATA_SANDBOX_PATH} not found, please use symlinks to make it available\"\n",
-    "\n",
-    "XENIUM_SDATA_PATH = os.path.join(SPATIALDATA_SANDBOX_PATH, \"xenium_rep1_io/data_aligned.zarr\")\n",
-    "VISIUM_SDATA_PATH = os.path.join(SPATIALDATA_SANDBOX_PATH, \"visium_associated_xenium_io/data_aligned.zarr\")\n",
+    "XENIUM_SDATA_PATH = \"visium_aligned.zarr\"\n",
+    "VISIUM_SDATA_PATH = \"xenium_aligned.zarr\"\n",
     "\n",
     "assert os.path.isdir(XENIUM_SDATA_PATH)\n",
     "assert os.path.isdir(VISIUM_SDATA_PATH)\n",

notebooks/examples/napari_rois.ipynb

@@ -65,6 +65,9 @@
      "start_time": "2023-04-10T21:55:20.519549Z"
     },
     "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    },
     "tags": []
    },
    "outputs": [],
@@ -85,10 +88,15 @@
    "id": "c9970140-afdd-499b-94f8-d6dd50792dac",
    "metadata": {
     "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    },
     "tags": []
    },
    "source": [
-    "You can download the data from here: [Visium dataset](https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zip). Please rename the file to `visium.zarr` and place it in the same folder as this notebook (or use symlinks to make the data accessible)."
+    "You can download the processed Visium data (already aligned) from here: [Visium dataset](https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io_aligned.zip). In alternative you can obtain the data by running [this analysis notebook](https://github.com/scverse/spatialdata-notebooks/blob/main/notebooks/paper_reproducibility/00_xenium_and_visium.ipynb).\n",
+    "\n",
+    "Please rename the file to `visium_aligned.zarr` and place it in the same folder as this notebook (or use symlinks to make the data accessible)."
    ]
   },
   {
@@ -100,7 +108,7 @@
    },
    "outputs": [],
    "source": [
-    "visium_sdata = sd.read_zarr(\"visium.zarr\")"
+    "visium_sdata = sd.read_zarr(\"visium_aligned.zarr\")"
    ]
   },
   {