oephys_visualization

oephys_visualization.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 44,
   "metadata": {},
   "outputs": [],
   "source": [
    "import h5py\n",
    "import numpy as np\n",
    "from matplotlib import pyplot as plt\n",
    "from ipywidgets import interact\n",
    "import io\n",
    "import shutil\n",
    "import tempfile\n",
    "import urllib.request\n",
    "import zipfile\n",
    "from IPython.core.display import HTML\n",
    "\n",
    "def oephys_plot(Recording):\n",
    "    %matplotlib widget \n",
    "    h5name = Recording + '_medium.h5'\n",
    "    with archive.open(h5name) as h5data:\n",
    "        with tempfile.SpooledTemporaryFile() as tmp_file:\n",
    "            shutil.copyfileobj(h5data, tmp_file)\n",
    "            with h5py.File(tmp_file,'r') as h:\n",
    "                dto = 1.0 * np.array(h['dto'])\n",
    "                dte = 1.0 * np.array(h['dte'])\n",
    "                quiroga = 1.0 * np.array(h['quiroga'])\n",
    "                dff = np.array(h['dff']).ravel()\n",
    "                sptimes = np.array(h['sptimes']).ravel()\n",
    "                genotype = h['genotype'][()].decode(\"utf-8\") \n",
    "                #V = np.array(h['ephys_raw']).ravel()\n",
    "                ephys = np.array(h['ephys_baseline_subtracted']).ravel()\n",
    "                fig, ax = plt.subplots(3, 1, sharex=True, sharey=False)\n",
    "                fig.set_figwidth(10)\n",
    "                fig.suptitle(Recording, fontsize=14)\n",
    "                ax[0].plot(np.arange(0,dff.size*dto,dto), dff, 'g')\n",
    "                ax[0].set_ylabel('DF/F')\n",
    "        #         ax[1].plot(np.arange(0,len(V)*dte,dte), 1000.0 * V, 'b')\n",
    "        #         ax[1].set_ylabel('V [mV]')\n",
    "                #ax[1].set_title('Raw cell-attached electrophysiology')\n",
    "                ax[1].plot(np.arange(0,len(ephys)*dte,dte), 1000.0 * ephys, 'k')\n",
    "                ax[1].set_ylabel('V [mV]')\n",
    "                ax[1].axhline(y=1000.0 * quiroga,  color = 'r', alpha = 0.5)\n",
    "                #ax[2].set_title('Post baseline-subtraction')\n",
    "                ax[2].eventplot(sptimes, orientation='horizontal', lineoffsets=-1, linelengths=0.5, linewidths=None, colors='r', linestyles='solid')\n",
    "                ax[2].set_xlabel('Time [s]')\n",
    "                ax[2].tick_params(labelleft=False) \n",
    "                display(HTML('<center><a href=' + data_dict[Recording] + '>Download the full data set ['+ Recording +'] in HDF5 format</a></center>'))\n",
    "\n",
    "archive = zipfile.ZipFile('oephys_medium.zip', 'r')\n",
    "\n",
    "\n",
    "cellids = ['102978','103467','102969','104001','102525','103444','102892','103992','103932','102510','102875','103920','103988','103402','103931','102890','102960','103863','102860','103950','102511','103991','103438','103406','103852','102891','102958','102086','104002','103953','102102','102906','102959','103979','103934','103933','103986','103985','102970','102529','103856','102858','103401','102512','103971','102956','103958','103849','103400','102898']\n",
    "url_list = ['https://www.dropbox.com/s/npahi5b2kg0li8s/102086.h5?dl=0', 'https://www.dropbox.com/s/v1q24t83hmv075k/102102.h5?dl=0', 'https://www.dropbox.com/s/6kafakjvfcj0k9i/102510.h5?dl=0', 'https://www.dropbox.com/s/wegiifv2glr2uym/102511.h5?dl=0', 'https://www.dropbox.com/s/lbeqfi2cn51bzr5/102512.h5?dl=0', 'https://www.dropbox.com/s/jsyhq7vu5329duj/102525.h5?dl=0', 'https://www.dropbox.com/s/58vrzxf7td85x8v/102529.h5?dl=0', 'https://www.dropbox.com/s/3b9wsf7nulxx5o4/102858.h5?dl=0', 'https://www.dropbox.com/s/u0aui5jiewfo9dx/102860.h5?dl=0', 'https://www.dropbox.com/s/oarz7pipcvxotv2/102875.h5?dl=0', 'https://www.dropbox.com/s/j3wuz64qwxlg2je/102890.h5?dl=0', 'https://www.dropbox.com/s/6n2axnjt19s21nh/102891.h5?dl=0', 'https://www.dropbox.com/s/5qh2o0gzt370ug0/102892.h5?dl=0', 'https://www.dropbox.com/s/ev6yzx3a5b7iwq9/102898.h5?dl=0', 'https://www.dropbox.com/s/sj2pul8k27kl45z/102906.h5?dl=0', 'https://www.dropbox.com/s/39i8rxr0ejc0rjr/102956.h5?dl=0', 'https://www.dropbox.com/s/8mx3fky55243vee/102958.h5?dl=0', 'https://www.dropbox.com/s/4k0lvi89u2qv4l3/102959.h5?dl=0', 'https://www.dropbox.com/s/rszu0jrafgohy8f/102960.h5?dl=0', 'https://www.dropbox.com/s/aw9gxcs4nfbs299/102969.h5?dl=0', 'https://www.dropbox.com/s/nizqswef6o3j81t/102970.h5?dl=0', 'https://www.dropbox.com/s/5h51iy0k92f1poi/102978.h5?dl=0', 'https://www.dropbox.com/s/iqw9iels8nqgyv7/103400.h5?dl=0', 'https://www.dropbox.com/s/x2f91h536j8qrk3/103401.h5?dl=0', 'https://www.dropbox.com/s/zswhxi9ck33oc18/103402.h5?dl=0', 'https://www.dropbox.com/s/99kvbfdjpf6avct/103406.h5?dl=0', 'https://www.dropbox.com/s/77yxcfth7h8ugft/103438.h5?dl=0', 'https://www.dropbox.com/s/5l49czden5ae75y/103444.h5?dl=0', 'https://www.dropbox.com/s/e9ugb1b1fhwj0bh/103467.h5?dl=0', 'https://www.dropbox.com/s/o7o5mnmqr9xpu1c/103849.h5?dl=0', 'https://www.dropbox.com/s/w0ajezbbsvy7tcc/103852.h5?dl=0', 'https://www.dropbox.com/s/tcjic1m64wmnyb0/103856.h5?dl=0', 'https://www.dropbox.com/s/m84bgaqn8sn715w/103863.h5?dl=0', 'https://www.dropbox.com/s/lbcmj0qbjy4y0ge/103920.h5?dl=0', 'https://www.dropbox.com/s/v8h7ne2fve9nly8/103931.h5?dl=0', 'https://www.dropbox.com/s/ikbb4z9lp5s6h3t/103932.h5?dl=0', 'https://www.dropbox.com/s/htz4nnr58jnqa8f/103933.h5?dl=0', 'https://www.dropbox.com/s/tp5o0fep8hw9upa/103934.h5?dl=0', 'https://www.dropbox.com/s/z8bsatb9tn9erom/103950.h5?dl=0', 'https://www.dropbox.com/s/hiq3uytvcebcs1v/103953.h5?dl=0', 'https://www.dropbox.com/s/tj0weua5u6rzww7/103958.h5?dl=0', 'https://www.dropbox.com/s/g71gg7cn171asbp/103971.h5?dl=0', 'https://www.dropbox.com/s/habsa5po24dlgn2/103979.h5?dl=0', 'https://www.dropbox.com/s/9e6bbxlaz60lmq6/103985.h5?dl=0', 'https://www.dropbox.com/s/qo8qujph9yn1vwy/103986.h5?dl=0', 'https://www.dropbox.com/s/gcavd8br3fu0j0x/103988.h5?dl=0', 'https://www.dropbox.com/s/iynuewvm3w22tpb/103991.h5?dl=0', 'https://www.dropbox.com/s/cj1fqbvp0zrv94s/103992.h5?dl=0', 'https://www.dropbox.com/s/t5gun7kdsyyjj54/104001.h5?dl=0', 'https://www.dropbox.com/s/iyh7kew5ypo3zwn/104002.h5?dl=0']\n",
    "Cre_lines = {'Cux2-f': ['104001','103992','103932','103920','103988','103931','103950','103991','104002','103953','103979','103934','103933','103986','103985','103971','103958'],'Emx1-f': ['102978','103467','102969','103444','103402','102960','103438','103406','102958','102959','102970','103401','102956',\n",
    "'103400'],'Emx1-s': ['102525','102892','102510','102875','102890','103863','102860','102511','103852','102891','102086','102102','102906','102529','103856','102858','102512','103849','102898']}\n",
    "data_dict = {}\n",
    "for url in url_list:\n",
    "    data_dict[url[-14:-8]] = url[:-1] + '1'\n",
    "    \n",
    "    \n",
    "##Cux2-f\n",
    "\n",
    "display(HTML('<center><h1> Visualization of downsampled calibration dataset </h1></center>')) \n",
    "display(HTML('<center><h2> Cux2-f (GCaMP6f) </h2></center>'))    \n",
    "interact(oephys_plot, Recording=Cre_lines['Cux2-f'])\n",
    "\n",
    "##Emx1-f\n",
    "display(HTML('<center><h2> Emx1-f (GCaMP6f) </h2></center>'))\n",
    "interact(oephys_plot, Recording=Cre_lines['Emx1-f'])\n",
    "\n",
    "##Emx1-s\n",
    "\n",
    "display(HTML('<center><h2> Emx1-s (GCaMP6s) </h2></center>'))\n",
    "interact(oephys_plot, Recording=Cre_lines['Emx1-s'])\n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "oephys",
   "language": "python",
   "name": "oephys"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.6.8"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}

postBuild

wget -q -O oephys_medium.zip "https://www.dropbox.com/s/7sv8op4f28gdua6/oephys_medium.zip?dl=1"

requirements.txt

bqplot
ipympl
ipyvolume
scipy
voila
h5py
numpy
matplotlib
ipywidgets