{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "See http://connectivity.brain-map.org/projection/experiment/168095756" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [], "source": [ "import json\n", "from allensdk.api.api import Api\n", "from allensdk.api.queries.rma_api import RmaApi\n", "from allensdk.api.queries.mouse_connectivity_api import MouseConnectivityApi\n", "import pandas as pd\n", "import itertools as it\n", "\n", "rma = RmaApi()\n", "mca = MouseConnectivityApi()\n", "\n", "def read_data(parsed_json):\n", " return parsed_json['msg']\n", "\n", "def pretty(result):\n", " print(json.dumps(result, indent=2))\n", " \n", "def tabular_dataframe(parsed_tabular_json):\n", " df = pd.DataFrame.from_records(parsed_tabular_json,\n", " columns=parsed_tabular_json[0].keys())\n", " return df" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": true }, "outputs": [], "source": [ "section_data_set_id = 168095756" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Manual Injection Summary\n", "Experiment: 168095756\n", "Primary Structure: Agranular insular area, posterior part\n", "Coords. (AP, ML, DV, L):\n", "\tBregma(-0.340000, 3.750000, 3.250000, 0.000000)\n", "\tBregma(-0.340000, 4.000000, 3.000000, 0.000000)\n", "Transgenic Line: Syt6-Cre_KI148\n", "Sparse, scattered expression in brain areas including the medulla, pons, and midbrain. Enriched in specific areas within thalamus, layer 6a cortex, and olfactory areas.\n" ] } ], "source": [ "# rma version from detail page\n", "results = mca.get_manual_injection_summary(section_data_set_id)\n", "\n", "print('Manual Injection Summary')\n", "print('Experiment: %d' % (results[0]['id']))\n", "injections = results[0]['specimen']['injections']\n", "print('Primary Structure: %s' % (injections[0]['structure']['name']))\n", "\n", "print('Coords. (AP, ML, DV, L):')\n", "for injection in injections:\n", " print ('\\t%s(%f, %f, %f, %f)' % (injection['registration_point'],\n", " injection['coordinates_ap'],\n", " injection['coordinates_ml'],\n", " injection['coordinates_dv'],\n", " injection['angle']))\n", "print('Transgenic Line: %s' % (results[0]['specimen']['donor']['transgenic_mouse']['transgenic_lines'][0]['name']))\n", "print(results[0]['specimen']['donor']['transgenic_mouse']['transgenic_lines'][0]['description'])\n", "\n" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "
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7.957860e+10 \n", "2196 168095756 0.000000e+00 2.303430e+10 \n", "2197 168095756 0.000000e+00 4.964210e+10 \n", "2198 168095756 8.200410e-04 1.907110e+09 \n", "\n", " projection_volume max_voxel_y max_voxel_x max_voxel_z id \\\n", "0 5.790980e-07 260 8280 4130 467146288 \n", "1 3.210740e-05 2440 6750 10340 467144044 \n", "2 5.905590e-04 6980 6020 4070 467143013 \n", "3 0.000000e+00 0 0 0 467143207 \n", "4 0.000000e+00 0 0 0 467147307 \n", "5 8.440580e-08 5250 8170 5570 467145633 \n", "6 0.000000e+00 0 0 0 467143091 \n", "7 1.095130e-03 7060 5150 4770 467146732 \n", "8 1.166760e-04 2400 10140 9640 467147588 \n", "9 5.009510e-07 2060 7350 5680 467143039 \n", "10 0.000000e+00 0 0 0 467143523 \n", "11 9.377850e-07 2060 7320 5780 467143946 \n", "12 0.000000e+00 0 0 0 467147201 \n", "13 0.000000e+00 0 0 0 467143359 \n", "14 1.556330e-05 4700 7000 7520 467146476 \n", "15 7.268850e-06 6920 10900 5850 467144287 \n", "16 8.963810e-09 1730 6040 9620 467145636 \n", "17 6.458410e-06 4420 11750 4600 467143316 \n", "18 3.931370e-06 4860 12390 6490 467144217 \n", "19 2.964320e-06 2860 4870 5710 467145304 \n", "20 0.000000e+00 0 0 0 467143102 \n", "21 3.845950e-04 5200 11750 8050 467143557 \n", "22 2.531590e-04 7070 10140 5630 467143225 \n", "23 9.773270e-06 5680 8360 5140 467143170 \n", "24 0.000000e+00 0 0 0 467143766 \n", "25 0.000000e+00 0 0 0 467147539 \n", "26 3.557270e-06 5610 7450 7950 467143900 \n", "27 0.000000e+00 0 0 0 467143131 \n", "28 4.467170e-04 7270 5420 8000 467146652 \n", "29 2.156960e-05 2360 10710 7580 467143462 \n", "... ... ... ... ... ... \n", "2169 1.055300e-04 4580 3490 8000 467144280 \n", "2170 0.000000e+00 0 0 0 467146754 \n", "2171 6.188350e-06 4240 3960 5700 467144117 \n", "2172 2.778470e-03 5190 4270 9490 467145467 \n", "2173 0.000000e+00 0 0 0 467142910 \n", "2174 5.833160e-07 3140 5670 6470 467143675 \n", "2175 0.000000e+00 0 0 0 467145228 \n", "2176 0.000000e+00 0 0 0 467143546 \n", "2177 0.000000e+00 0 0 0 467143855 \n", "2178 1.909260e-05 7120 5760 7510 467144167 \n", "2179 8.912480e-04 5260 5740 9830 467145572 \n", "2180 9.802790e-08 5350 10220 5760 467145710 \n", "2181 0.000000e+00 0 0 0 467144704 \n", "2182 0.000000e+00 0 0 0 467144717 \n", "2183 2.899730e-02 4600 5720 9490 467145854 \n", "2184 7.454270e-06 3070 9070 740 467143045 \n", "2185 1.341720e-05 6830 12760 4060 467143339 \n", "2186 0.000000e+00 0 0 0 467143967 \n", "2187 5.994830e-04 5200 11750 8050 467145548 \n", "2188 0.000000e+00 0 0 0 467147591 \n", "2189 2.228910e-04 1840 5350 9440 467144076 \n", "2190 3.354000e-04 1900 2360 6660 467144918 \n", "2191 2.589350e-05 6210 7850 4450 467146315 \n", "2192 0.000000e+00 0 0 0 467143354 \n", "2193 0.000000e+00 0 0 0 467144219 \n", "2194 1.348090e-06 2510 9470 1160 467143454 \n", "2195 0.000000e+00 0 0 0 467143299 \n", "2196 0.000000e+00 0 0 0 467143653 \n", "2197 0.000000e+00 0 0 0 467145216 \n", "2198 1.333720e-05 6210 7850 4450 467142721 \n", "\n", " normalized_projection_volume \n", "0 0.000750 \n", "1 0.041564 \n", "2 0.764488 \n", "3 0.000000 \n", "4 0.000000 \n", "5 0.000109 \n", "6 0.000000 \n", "7 1.417670 \n", "8 0.151040 \n", "9 0.000648 \n", "10 0.000000 \n", "11 0.001214 \n", "12 0.000000 \n", "13 0.000000 \n", "14 0.020147 \n", "15 0.009410 \n", "16 0.000012 \n", "17 0.008361 \n", "18 0.005089 \n", "19 0.003837 \n", "20 0.000000 \n", "21 0.497865 \n", "22 0.327719 \n", "23 0.012652 \n", "24 0.000000 \n", "25 0.000000 \n", "26 0.004605 \n", "27 0.000000 \n", "28 0.578282 \n", "29 0.027922 \n", "... ... \n", "2169 0.136610 \n", "2170 0.000000 \n", "2171 0.008011 \n", "2172 3.596780 \n", "2173 0.000000 \n", "2174 0.000755 \n", "2175 0.000000 \n", "2176 0.000000 \n", "2177 0.000000 \n", "2178 0.024716 \n", "2179 1.153730 \n", "2180 0.000127 \n", "2181 0.000000 \n", "2182 0.000000 \n", "2183 37.537500 \n", "2184 0.009650 \n", "2185 0.017369 \n", "2186 0.000000 \n", "2187 0.776040 \n", "2188 0.000000 \n", "2189 0.288536 \n", "2190 0.434180 \n", "2191 0.033520 \n", "2192 0.000000 \n", "2193 0.000000 \n", "2194 0.001745 \n", "2195 0.000000 \n", "2196 0.000000 \n", "2197 0.000000 \n", "2198 0.017265 \n", "\n", "[2199 rows x 19 columns]" ] }, "execution_count": 4, "metadata": {}, "output_type": "execute_result" } ], "source": [ "projection_results = mca.get_structure_unionizes([section_data_set_id], is_injection=False)\n", "projection_df = tabular_dataframe(projection_results)\n", "projection_df" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "
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st_levelgraph_idnameweightacronymparent_structure_idgraph_ordersphinx_idhemisphere_idsafe_name...faileddepthneuro_name_structure_id_pathneuro_name_structure_idstructure_name_facetfailed_facetidontology_idatlas_idstructure_set_ancestor
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1 rows × 22 columns

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" ], "text/plain": [ " st_level graph_id name weight acronym parent_structure_id \\\n", "377 NaN 1 Piriform area 8690 PIR 698 \n", "\n", " graph_order sphinx_id hemisphere_id safe_name \\\n", "377 377 378 3 Piriform area \n", "\n", " ... failed depth \\\n", "377 ... False 6 \n", "\n", " neuro_name_structure_id_path neuro_name_structure_id \\\n", "377 None None \n", "\n", " structure_name_facet failed_facet id ontology_id atlas_id \\\n", "377 3867654445 734881840 961 1 261 \n", "\n", " structure_set_ancestor \n", "377 [997, 8, 567, 688, 695, 698, 961] \n", "\n", "[1 rows x 22 columns]" ] }, "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ "from allensdk.api.queries.ontologies_api import OntologiesApi\n", "oa = OntologiesApi()\n", "\n", "atlases = tabular_dataframe(oa.get_atlases_table(brief=True))\n", "mouse_p56_coronal_id = atlases[atlases.name == 'Mouse, P56, Coronal']['structure_graph'].iloc[0]['id'] # 1\n", "\n", "# calculate a list of only the ancestors that are in the limited structure set\n", "structure_set_df = tabular_dataframe(oa.get_structures(mouse_p56_coronal_id))\n", "\n", "oa.unpack_structure_set_ancestors(structure_set_df)\n", "\n", "structure_set_df[structure_set_df.acronym == 'PIR']" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/home/timf/anaconda/lib/python2.7/site-packages/pandas/core/frame.py:1825: UserWarning: Boolean Series key will be reindexed to match DataFrame index.\n", " \"DataFrame index.\", UserWarning)\n" ] }, { "data": { "text/html": [ "
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hemisphere_idstructure_idprojection_volumeidacronymgraph_order
019970.020088997root0
129970.062792997root0
2180.0153018grey1
3280.0585388grey1
425670.046989567CH2
526880.045993688CTX3
626950.043597695CTXpl4
723150.028033315Isocortex5
82950.01594795AI260
921110.009313111AIp267
1029220.005093922PERI328
1126980.011002698OLF340
1229610.008747961PIR377
1313430.010513343BS588
1423430.011057343BS588
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" ], "text/plain": [ " hemisphere_id structure_id projection_volume id acronym \\\n", "0 1 997 0.020088 997 root \n", "1 2 997 0.062792 997 root \n", "2 1 8 0.015301 8 grey \n", "3 2 8 0.058538 8 grey \n", "4 2 567 0.046989 567 CH \n", "5 2 688 0.045993 688 CTX \n", "6 2 695 0.043597 695 CTXpl \n", "7 2 315 0.028033 315 Isocortex \n", "8 2 95 0.015947 95 AI \n", "9 2 111 0.009313 111 AIp \n", "10 2 922 0.005093 922 PERI \n", "11 2 698 0.011002 698 OLF \n", "12 2 961 0.008747 961 PIR \n", "13 1 343 0.010513 343 BS \n", "14 2 343 0.011057 343 BS \n", "\n", " graph_order \n", "0 0 \n", "1 0 \n", "2 1 \n", "3 1 \n", "4 2 \n", "5 3 \n", "6 4 \n", "7 5 \n", "8 260 \n", "9 267 \n", "10 328 \n", "11 340 \n", "12 377 \n", "13 588 \n", "14 588 " ] }, "execution_count": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ "cutoff = 0.0050\n", "data_field = 'projection_volume'\n", "\n", "# projection joined to structures\n", "table = pd.concat((\n", " pd.merge(projection_df[projection_df.hemisphere_id == h]\n", " [projection_df.projection_volume > cutoff].loc[:,['hemisphere_id',\n", " 'structure_id',\n", " data_field]],\n", " structure_set_df[['id','acronym','graph_order']],\n", " how='inner',\n", " left_on='structure_id', right_on='id')\n", " for h in [1, 2])).sort('graph_order').\\\n", " reset_index('structure_id', 'hemisphere_id')\n", " \n", "table[['acronym', 'hemisphere_id', 'projection_volume']]\n", "\n", "table" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "
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structureLR
graph_order
0root0.0200880.062792
1grey0.0153010.058538
2CHNaN0.046989
3CTXNaN0.045993
4CTXplNaN0.043597
5IsocortexNaN0.028033
260AINaN0.015947
267AIpNaN0.009313
328PERINaN0.005093
340OLFNaN0.011002
377PIRNaN0.008747
588BS0.0105130.011057
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" ], "text/plain": [ " structure L R\n", "graph_order \n", "0 root 0.020088 0.062792\n", "1 grey 0.015301 0.058538\n", "2 CH NaN 0.046989\n", "3 CTX NaN 0.045993\n", "4 CTXpl NaN 0.043597\n", "5 Isocortex NaN 0.028033\n", "260 AI NaN 0.015947\n", "267 AIp NaN 0.009313\n", "328 PERI NaN 0.005093\n", "340 OLF NaN 0.011002\n", "377 PIR NaN 0.008747\n", "588 BS 0.010513 0.011057" ] }, "execution_count": 8, "metadata": {}, "output_type": "execute_result" } ], "source": [ "display_table = table.loc[:,['acronym', 'hemisphere_id', 'projection_volume', 'graph_order']].pivot(index='graph_order',\n", " columns='hemisphere_id').iloc[:,1:]\n", "\n", "display_table.columns = ['structure','L', 'R']\n", "display_table" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 2", "language": "python", "name": "python2" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 2 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython2", "version": "2.7.10" } }, "nbformat": 4, "nbformat_minor": 0 }