update links

templates_ark/4_Post_Clustering.ipynb

@@ -184,7 +184,7 @@
    "metadata": {},
    "source": [
     "### Manual inspection of problematic clusters with Mantis\n",
-    "Once you've pulled out the problematic cells into new clusters, you'll need to visually inspect them to determine which cluster they belong to. The code below will create a directory to enable easy visualization with Mantis Viewer. See the [Mantis section of the README](https://github.com/angelolab/ark-analysis#mantis) for an overview of how to use Mantis. You can then manually inspect each of the newly created clusters to determine what the true cell type is."
+    "Once you've pulled out the problematic cells into new clusters, you'll need to visually inspect them to determine which cluster they belong to. The code below will create a directory to enable easy visualization with Mantis Viewer. See the [Mantis section of the README](../README.md#mantis-viewer) for an overview of how to use Mantis. You can then manually inspect each of the newly created clusters to determine what the true cell type is."
    ]
   },
   {
@@ -336,7 +336,7 @@
    "metadata": {},
    "source": [
     "### Manually inspect images to confirm\n",
-    "Once you've identified a plausible threshold for the specified marker, it's time to look at the images in Mantis. In each image, identify the cells that are positive for the specified marker, and determine what their expression level is. Then, do the same thing for the cells that are negative for the marker. By performing this across a representative range of images, it is straightforward to come up with an estimate of what threshold accurately descriminates between positive and negative cells. You'll need to first [load the marker_counts.csv file](https://github.com/angelolab/ark-analysis#loading_project_wide_files) into Mantis. Then, once it's been loaded, you can [view the expression](https://github.com/angelolab/ark-analysis#view_cell_features) of the specified marker for the cells in the image. "
+    "Once you've identified a plausible threshold for the specified marker, it's time to look at the images in Mantis. In each image, identify the cells that are positive for the specified marker, and determine what their expression level is. Then, do the same thing for the cells that are negative for the marker. By performing this across a representative range of images, it is straightforward to come up with an estimate of what threshold accurately descriminates between positive and negative cells. You'll need to first [load the marker_counts.csv file](../README.md#loading_project_wide_files) into Mantis. Then, once it's been loaded, you can [view the expression](../README.md#view_cell_features) of the specified marker for the cells in the image. "
    ]
   },
   {