diff --git a/examples/loading_data/loading_raw_ephys_data.ipynb b/examples/loading_data/loading_raw_ephys_data.ipynb index 42cfb3517..9394b675e 100644 --- a/examples/loading_data/loading_raw_ephys_data.ipynb +++ b/examples/loading_data/loading_raw_ephys_data.ipynb @@ -328,55 +328,57 @@ }, { "cell_type": "markdown", + "id": "723df072", + "metadata": {}, "source": [ "## Get the probe geometry" - ], - "metadata": { - "collapsed": false - } + ] }, { "cell_type": "markdown", + "id": "35a0db60", + "metadata": {}, "source": [ "### Using the `eid` and `probe` information" - ], - "metadata": { - "collapsed": false - } + ] }, { "cell_type": "code", "execution_count": null, + "id": "c2335beb", + "metadata": {}, "outputs": [], "source": [ "from brainbox.io.one import load_channel_locations\n", - "channels = load_channel_locations(eid, probe)\n", - "channels[probe][\"localCoordinates\"]" - ], - "metadata": { - "collapsed": false - } + "from one.api import ONE\n", + "import spikeglx\n", + "import numpy as np\n", + "one = ONE()\n", + "\n", + "pid = 'da8dfec1-d265-44e8-84ce-6ae9c109b8bd'\n", + "eid, probe = one.pid2eid(pid)\n", + "channels = load_channel_locations(eid, probe)[probe]\n", + "channel_geometry = np.c_[channels['axial_um'], channels['lateral_um']]" + ] }, { "cell_type": "markdown", + "id": "360f668c", + "metadata": {}, "source": [ "### Using the reader and the `.cbin` file" - ], - "metadata": { - "collapsed": false - } + ] }, { "cell_type": "code", "execution_count": null, + "id": "763d6ac8", + "metadata": {}, "outputs": [], "source": [ "sr = spikeglx.Reader(bin_file)\n", "sr.geometry" - ], - "metadata": { - "collapsed": false - } + ] }, { "cell_type": "markdown", @@ -395,9 +397,9 @@ "metadata": { "celltoolbar": "Edit Metadata", "kernelspec": { - "display_name": "Python [conda env:iblenv] *", + "display_name": "Python 3 (ipykernel)", "language": "python", - "name": "conda-env-iblenv-py" + "name": "python3" }, "language_info": { "codemirror_mode": { @@ -409,7 +411,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.7" + "version": "3.9.16" } }, "nbformat": 4,