Neuropixel probes

.github/workflows/build.yml

@@ -25,7 +25,7 @@ jobs:
         run: pip freeze
 
       - name: Installing requirements
-        run: pip install -r requirements.txt --user
+        run: pip install -r .binder/requirements.txt --user
 
       - name: Installing build dependencies
         run: |

.gitignore

@@ -1,3 +1,4 @@
 *.ipynb_checkpoints*
 *_build
 *nwb-cache
+*.nwb

docs/intro.md

@@ -10,6 +10,7 @@ Reproducible Analysis requires four components;
 - Accessible Computational Resources
 - Reproducible environment
 - Documentation of Usage
+
 This Databook leverages a number of technologies to combine those components into a web-application. 
 
 ### Data

docs/visualization/visualize_neuropixel_probes.ipynb

@@ -5,6 +5,14 @@
    "metadata": {},
    "source": [
     "# Visualizing Neuropixel Probe Locations\n",
+    "\n",
+    "**Note: This notebook currently doesn't work on remote locations. To run it, it should be downloaded and run locally. Instructions for this can be found on the [Main Page](../intro.md)**"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
     "It can be handy to know the location and trajectory of the probes that obtain the data. Some NWB files have an **electrodes** field which store these locations. To be more precise, they contain arrays of **CCF** coordinates. [CCF](https://community.brain-map.org/t/allen-mouse-ccf-accessing-and-using-related-data-and-tools/359) is a framework which allows us to represent locations in the brain with coordinates that are relative to brain structure. This notebook uses CCF coordinate data in an extracellular electrophysiology NWB file to render the locations of the [Neuropixel](https://www.neuropixels.org/probe) probes that were used.\n",
     "\n",
     "To be able to render locations in a brain, you don't need to know how CCF works except that it is a system of coordinates. We use **[ccf-widget](https://github.com/NeurodataWithoutBorders/ccf-widget)** as the engine by which we 3D render the brain and the probe coordinates."