{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "See http://connectivity.brain-map.org/projection/experiment/168095756" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": true }, "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": 9, "metadata": { "collapsed": true }, "outputs": [], "source": [ "section_data_set_id = 168095756" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "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", "\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": 11, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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2520 rows × 19 columns

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3.266868e+10 \n", "2493 168095756 0.000000e+00 1.957360e+10 \n", "2494 168095756 5.343333e-08 4.411985e+11 \n", "2495 168095756 7.812257e-06 4.001790e+11 \n", "2496 168095756 0.000000e+00 1.964243e+11 \n", "2497 168095756 0.000000e+00 1.036625e+10 \n", "2498 168095756 0.000000e+00 6.719913e+10 \n", "2499 168095756 0.000000e+00 1.868418e+09 \n", "2500 168095756 0.000000e+00 8.952062e+09 \n", "2501 168095756 6.147416e-05 2.920324e+11 \n", "2502 168095756 0.000000e+00 1.548432e+11 \n", "2503 168095756 1.408416e-05 2.280057e+11 \n", "2504 168095756 9.196754e-05 2.355656e+09 \n", "2505 168095756 0.000000e+00 7.699984e+10 \n", "2506 168095756 0.000000e+00 1.998740e+11 \n", "2507 168095756 3.020437e-06 4.008319e+10 \n", "2508 168095756 0.000000e+00 8.502156e+10 \n", "2509 168095756 0.000000e+00 5.162894e+09 \n", "2510 168095756 0.000000e+00 9.787314e+10 \n", "2511 168095756 1.192491e-05 1.197024e+12 \n", "2512 168095756 7.969890e-08 3.735597e+11 \n", "2513 168095756 0.000000e+00 8.493145e+10 \n", "2514 168095756 6.478206e-05 8.528342e+11 \n", "2515 168095756 3.208120e-06 2.519184e+10 \n", "2516 168095756 5.802552e-06 3.043328e+09 \n", "2517 168095756 3.692963e-05 2.328922e+10 \n", "2518 168095756 2.549023e-04 8.258442e+12 \n", "2519 168095756 0.000000e+00 1.545278e+11 \n", "\n", " projection_volume max_voxel_y max_voxel_x max_voxel_z id \\\n", "0 0.000000e+00 0 0 0 630134710 \n", "1 1.326879e-05 3250 6100 6300 630137423 \n", "2 1.608324e-04 4380 4430 1550 630136438 \n", "3 0.000000e+00 0 0 0 630135976 \n", "4 0.000000e+00 0 0 0 630135291 \n", "5 6.058290e-06 5050 9960 5870 630137684 \n", "6 0.000000e+00 0 0 0 630135861 \n", "7 0.000000e+00 0 0 0 630134576 \n", "8 1.017496e-04 5090 8690 3470 630135630 \n", "9 0.000000e+00 0 0 0 630134462 \n", "10 0.000000e+00 0 0 0 630136119 \n", "11 0.000000e+00 0 0 0 630136310 \n", "12 0.000000e+00 0 0 0 630137696 \n", "13 5.017976e-07 3030 13160 6710 630137544 \n", "14 8.122528e-04 3780 2410 7050 630134593 \n", "15 3.962530e-05 1880 10190 8020 630134900 \n", "16 0.000000e+00 0 0 0 630136418 \n", "17 0.000000e+00 0 0 0 630135296 \n", "18 1.146376e-04 4350 10140 2940 630135725 \n", "19 0.000000e+00 0 0 0 630136721 \n", "20 0.000000e+00 0 0 0 630135624 \n", "21 5.632192e-06 7090 9760 4650 630136604 \n", "22 0.000000e+00 0 0 0 630135374 \n", "23 4.316161e-07 2860 4330 7240 630137677 \n", "24 3.103463e-03 7070 5880 4000 630135968 \n", "25 0.000000e+00 0 0 0 630136524 \n", "26 1.598158e-06 1220 10960 4560 630135840 \n", "27 5.790707e-08 390 6910 7480 630136225 \n", "28 1.945466e-04 3770 9570 940 630135847 \n", "29 1.054928e-02 5960 9270 3510 630137602 \n", "... ... ... ... ... ... \n", "2490 3.179177e-06 3030 7970 610 630135621 \n", "2491 9.143327e-05 4730 740 5690 630135604 \n", "2492 1.882014e-06 5790 6110 5660 630136521 \n", "2493 0.000000e+00 0 0 0 630136169 \n", "2494 1.188491e-07 3940 5880 6110 630136964 \n", "2495 1.079279e-05 4860 12740 8000 630135088 \n", "2496 0.000000e+00 0 0 0 630134489 \n", "2497 0.000000e+00 0 0 0 630134468 \n", "2498 0.000000e+00 0 0 0 630136198 \n", "2499 0.000000e+00 0 0 0 630135364 \n", "2500 0.000000e+00 0 0 0 630135910 \n", "2501 8.161931e-05 2100 5830 5670 630136429 \n", "2502 0.000000e+00 0 0 0 630136926 \n", "2503 1.949411e-05 3030 10000 9970 630137121 \n", "2504 5.203247e-06 5010 12570 7530 630136337 \n", "2505 0.000000e+00 0 0 0 630137530 \n", "2506 0.000000e+00 0 0 0 630135802 \n", "2507 3.176164e-06 1410 7880 4420 630136963 \n", "2508 0.000000e+00 0 0 0 630136799 \n", "2509 0.000000e+00 0 0 0 630136518 \n", "2510 0.000000e+00 0 0 0 630134485 \n", "2511 8.783289e-05 3440 9020 8100 630137482 \n", "2512 1.163199e-07 1390 10170 4420 630137444 \n", "2513 0.000000e+00 0 0 0 630134777 \n", "2514 5.966988e-04 6350 8640 5620 630135901 \n", "2515 4.802616e-07 6500 7980 5950 630137769 \n", "2516 1.501641e-07 6700 6170 7210 630134560 \n", "2517 9.896006e-06 2640 7640 5800 630135226 \n", "2518 1.248409e-02 5440 5750 9630 630137313 \n", "2519 0.000000e+00 0 0 0 630137691 \n", "\n", " normalized_projection_volume \n", "0 0.000000 \n", "1 0.016267 \n", "2 0.197175 \n", "3 0.000000 \n", "4 0.000000 \n", "5 0.007427 \n", "6 0.000000 \n", "7 0.000000 \n", "8 0.124742 \n", "9 0.000000 \n", "10 0.000000 \n", "11 0.000000 \n", "12 0.000000 \n", "13 0.000615 \n", "14 0.995796 \n", "15 0.048579 \n", "16 0.000000 \n", "17 0.000000 \n", "18 0.140542 \n", "19 0.000000 \n", "20 0.000000 \n", "21 0.006905 \n", "22 0.000000 \n", "23 0.000529 \n", "24 3.804746 \n", "25 0.000000 \n", "26 0.001959 \n", "27 0.000071 \n", "28 0.238508 \n", "29 12.933080 \n", "... ... \n", "2490 0.003898 \n", "2491 0.112094 \n", "2492 0.002307 \n", "2493 0.000000 \n", "2494 0.000146 \n", "2495 0.013232 \n", "2496 0.000000 \n", "2497 0.000000 \n", "2498 0.000000 \n", "2499 0.000000 \n", "2500 0.000000 \n", "2501 0.100063 \n", "2502 0.000000 \n", "2503 0.023899 \n", "2504 0.006379 \n", "2505 0.000000 \n", "2506 0.000000 \n", "2507 0.003894 \n", "2508 0.000000 \n", "2509 0.000000 \n", "2510 0.000000 \n", "2511 0.107680 \n", "2512 0.000143 \n", "2513 0.000000 \n", "2514 0.731534 \n", "2515 0.000589 \n", "2516 0.000184 \n", "2517 0.012132 \n", "2518 15.305088 \n", "2519 0.000000 \n", "\n", "[2520 rows x 19 columns]" ] }, "execution_count": 11, "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": 12, "metadata": {}, "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
41681Piriform area8690PIR698.04164173Piriform area...False6NoneNone38676544457348818409611261.0[997, 8, 567, 688, 695, 698, 961]
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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", "416 8 1 Piriform area 8690 PIR 698.0 \n", "\n", " graph_order sphinx_id hemisphere_id safe_name \\\n", "416 416 417 3 Piriform area \n", "\n", " ... failed depth \\\n", "416 ... False 6 \n", "\n", " neuro_name_structure_id_path neuro_name_structure_id \\\n", "416 None None \n", "\n", " structure_name_facet failed_facet id ontology_id atlas_id \\\n", "416 3867654445 734881840 961 1 261.0 \n", "\n", " structure_set_ancestor \n", "416 [997, 8, 567, 688, 695, 698, 961] \n", "\n", "[1 rows x 22 columns]" ] }, "execution_count": 12, "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": 13, "metadata": { "scrolled": true }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/home/nicholasc/anaconda2/lib/python2.7/site-packages/ipykernel_launcher.py:13: UserWarning: Boolean Series key will be reindexed to match DataFrame index.\n", " del sys.path[0]\n" ] }, { "data": { "text/html": [ "
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hemisphere_idprojection_volumeidacronymgraph_order
structure_id
99710.026879997root0
99720.069915997root0
810.0110548grey1
820.0546408grey1
56720.046495567CH2
68820.045730688CTX3
69520.043994695CTXpl4
31520.028471315Isocortex5
9520.01759195AI278
11120.011202111AIp285
69820.011256698OLF379
96120.010141961PIR416
34320.007112343BS639
34310.006532343BS639
106510.0056471065HB882
106520.0064381065HB882
35420.005571354MY935
35410.005050354MY935
100910.0055691009fiber tracts1101
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" ], "text/plain": [ " hemisphere_id projection_volume id acronym \\\n", "structure_id \n", "997 1 0.026879 997 root \n", "997 2 0.069915 997 root \n", "8 1 0.011054 8 grey \n", "8 2 0.054640 8 grey \n", "567 2 0.046495 567 CH \n", "688 2 0.045730 688 CTX \n", "695 2 0.043994 695 CTXpl \n", "315 2 0.028471 315 Isocortex \n", "95 2 0.017591 95 AI \n", "111 2 0.011202 111 AIp \n", "698 2 0.011256 698 OLF \n", "961 2 0.010141 961 PIR \n", "343 2 0.007112 343 BS \n", "343 1 0.006532 343 BS \n", "1065 1 0.005647 1065 HB \n", "1065 2 0.006438 1065 HB \n", "354 2 0.005571 354 MY \n", "354 1 0.005050 354 MY \n", "1009 1 0.005569 1009 fiber tracts \n", "\n", " graph_order \n", "structure_id \n", "997 0 \n", "997 0 \n", "8 1 \n", "8 1 \n", "567 2 \n", "688 3 \n", "695 4 \n", "315 5 \n", "95 278 \n", "111 285 \n", "698 379 \n", "961 416 \n", "343 639 \n", "343 639 \n", "1065 882 \n", "1065 882 \n", "354 935 \n", "354 935 \n", "1009 1101 " ] }, "execution_count": 13, "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_values('graph_order').set_index('structure_id')\n", " \n", "# table[['acronym', 'hemisphere_id', 'projection_volume']]\n", "\n", "table" ] }, { "cell_type": "code", "execution_count": 14, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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hemisphere_idLRLR
graph_order
0rootroot0.0268790.069915
1greygrey0.0110540.054640
2NaNCHNaN0.046495
3NaNCTXNaN0.045730
4NaNCTXplNaN0.043994
5NaNIsocortexNaN0.028471
278NaNAINaN0.017591
285NaNAIpNaN0.011202
379NaNOLFNaN0.011256
416NaNPIRNaN0.010141
639BSBS0.0065320.007112
882HBHB0.0056470.006438
935MYMY0.0050500.005571
1101fiber tractsNaN0.005569NaN
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" ], "text/plain": [ "hemisphere_id L R L R\n", "graph_order \n", "0 root root 0.026879 0.069915\n", "1 grey grey 0.011054 0.054640\n", "2 NaN CH NaN 0.046495\n", "3 NaN CTX NaN 0.045730\n", "4 NaN CTXpl NaN 0.043994\n", "5 NaN Isocortex NaN 0.028471\n", "278 NaN AI NaN 0.017591\n", "285 NaN AIp NaN 0.011202\n", "379 NaN OLF NaN 0.011256\n", "416 NaN PIR NaN 0.010141\n", "639 BS BS 0.006532 0.007112\n", "882 HB HB 0.005647 0.006438\n", "935 MY MY 0.005050 0.005571\n", "1101 fiber tracts NaN 0.005569 NaN" ] }, "execution_count": 14, "metadata": {}, "output_type": "execute_result" } ], "source": [ "display_table = table[['hemisphere_id', 'acronym', 'projection_volume', 'graph_order']].pivot(index='graph_order', columns='hemisphere_id')\n", "# display_table.columns = ['structure','L', 'R']\n", "display_table.columns = display_table.columns.droplevel(0)\n", "display_table.rename(columns={1:'L', 2:'R'})" ] } ], "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": "2.7.15" } }, "nbformat": 4, "nbformat_minor": 1 }