From 1f0642149a61236e8654f7a4cd9167173678f539 Mon Sep 17 00:00:00 2001 From: Carter Peene Date: Tue, 20 Dec 2022 12:39:39 -0800 Subject: [PATCH 1/4] Update build to use relocated requirements.txt --- .github/workflows/build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 34bffa6f..450a59d1 100644 --- a/.github/workflows/build.yml +++ b/.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: | From 801a7f8f47dc09773dcc4218cb8127d649f99e0e Mon Sep 17 00:00:00 2001 From: Carter Peene Date: Tue, 20 Dec 2022 14:48:45 -0800 Subject: [PATCH 2/4] Update .gitignore --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 2add7fa7..834bee5a 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,4 @@ *.ipynb_checkpoints* *_build *nwb-cache +*.nwb From ad1a69e77cd3fee969933bac57823de3067dd230 Mon Sep 17 00:00:00 2001 From: Carter Peene Date: Tue, 3 Jan 2023 16:46:56 -0800 Subject: [PATCH 3/4] Update intro.md --- docs/intro.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/intro.md b/docs/intro.md index 95d06c61..c70cb8c1 100644 --- a/docs/intro.md +++ b/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 From ffa341af0fec97f23f313c9494987e3c77fd8f24 Mon Sep 17 00:00:00 2001 From: Carter Peene Date: Fri, 6 Jan 2023 12:52:52 -0800 Subject: [PATCH 4/4] Added disclaimer to notebook that it currently doesnt work on remote locations --- docs/visualization/visualize_neuropixel_probes.ipynb | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/docs/visualization/visualize_neuropixel_probes.ipynb b/docs/visualization/visualize_neuropixel_probes.ipynb index fc293ff8..c512f74b 100644 --- a/docs/visualization/visualize_neuropixel_probes.ipynb +++ b/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."