Fixed Pablo's comments

CamaraLab · Jan 9, 2025 · f3a3e92 · f3a3e92
1 parent 99eaca7
commit f3a3e92
Showing 1 changed file with 4 additions and 5 deletions.
diff --git a/docs/notebooks/Example_1.ipynb b/docs/notebooks/Example_1.ipynb
@@ -43,8 +43,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# bd = \"/home/jovyan/\" # Base directory\n",
-    "bd = \"/home/patn/dropbox/Data/AllenInstitute\""
+    "bd = \"/home/jovyan/\" # Base directory"
    ]
   },
   {
@@ -510,11 +509,11 @@
    "id": "9d1b72ab",
    "metadata": {},
    "source": [
-    "Another tool CAJAL offers to better understand the morphology characteristics of a cell cluster is an \"average spanning tree\" algorithm, which takes as input a cluster of morphologically similar neurons and returns a topological tree structure which is representative of the topology and branching characteristics of cells in the cluster; visualizing this tree can give intuition into the basic commonalities in the cluster.\n",
+    "Another tool CAJAL offers to better understand the morphological characteristics of a cluster of cells is an \"average spanning tree\" algorithm, which takes as input a cluster of morphologically similar neurons and returns a topological tree structure which is representative of the topology and branching characteristics of cells in the cluster; visualizing this tree can give intuition into the basic commonalities in the cluster.\n",
     "\n",
-    "The concept behind the algorithm is that, since the Gromov-Wasserstein offers a way to align cells with each other, after identifying the medoid cell of the cluster, we can align the other cells with the medoid cells using the optimal transport plans, which makes it possible to superimpose the graphs in a meaningful way and literally take the arithmetic average of their adjacency matrices.\n",
+    "The concept behind the algorithm is that, since the Gromov-Wasserstein distance offers a way to align cells with each other, after identifying the medoid cell of the cluster, we can align the cells with the medoid cell using the optimal transport plans, which makes it possible to superimpose the graphs in a meaningful way and take the arithmetic average of their adjacency matrices.\n",
     "\n",
-    "The graph can be visualized with any standard Python graph library, we illustrate the usage here with Networkx."
+    "The graph can be visualized with any standard Python graph library, such as Networkx. We illustrate the usage here with the computation of the average spanning tree for cells in cluster 0,"
    ]
   },
   {