{ "cells": [ { "cell_type": "raw", "metadata": { "raw_mimetype": "text/restructuredtext" }, "source": [ "Calculating user contributions\n", "==============================\n", "\n", "When gearing up for publication, you will find that due to the collaborative approach of CATMAID a great many people will have contributed to the data you would like to publish. In order to come up with a sensible author list, it is useful to quantify how much a user has contributed to the reconstruction of a set of neurons. CATMAID provides you a broad summary of contributions e.g. via the selection table. Pymaid let's you fetch that data and more.\n", "\n", "First, let's get a set of olfactory projection neurons to demonstrate user statistics on:" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "INFO : Found 9 skeletons with matching annotation(s) (pymaid)\n" ] } ], "source": [ "import pymaid\n", "\n", "# Initialize connection\n", "rm = pymaid.connect_catmaid()\n", "\n", "# Fetch some neurons\n", "nl = pymaid.get_neurons('annotation:glomerulus DA1 right')" ] }, { "cell_type": "raw", "metadata": { "raw_mimetype": "text/restructuredtext" }, "source": [ "First some basic stats:" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | skeleton_id | \n", "n_nodes | \n", "node_contributors | \n", "n_presynapses | \n", "pre_contributors | \n", "n_postsynapses | \n", "post_contributors | \n", "review_contributors | \n", "multiuser_review_minutes | \n", "construction_minutes | \n", "min_review_minutes | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "61221 | \n", "7875 | \n", "{'adamjohn': 2442, 'ranftp': 4109, 'ratliffj':... | \n", "404 | \n", "{'hsuj': 1, 'adamjohn': 10, 'ranftp': 249, 'ha... | \n", "128 | \n", "{'ranftp': 89, 'alij': 1, 'koppenhaverb': 5, '... | \n", "{'ratliffj': 2834, 'masoodpanahn': 84, 'koppen... | \n", "165 | \n", "416 | \n", "135 | \n", "
1 | \n", "27295 | \n", "9975 | \n", "{'koppenhaverb': 102, 'robertsr': 53, 'lovef':... | \n", "412 | \n", "{'robertsr': 32, 'alij': 6, 'schlegelp': 205, ... | \n", "59 | \n", "{'alij': 2, 'heatha': 2, 'hallouc': 2, 'schleg... | \n", "{'schlegelp': 517, 'adesinaa': 2586, 'kmecoval... | \n", "367 | \n", "502 | \n", "313 | \n", "
2 | \n", "57323 | \n", "4585 | \n", "{'kmecoval': 2194, 'robertsr': 159, 'koppenhav... | \n", "361 | \n", "{'calles': 2, 'michaelLingelbach': 1, 'kmecova... | \n", "76 | \n", "{'vallas': 1, 'ranftp': 1, 'edmondsona': 20, '... | \n", "{'ratliffj': 2116, 'kmecoval': 350, 'masoodpan... | \n", "176 | \n", "208 | \n", "84 | \n", "
3 | \n", "57311 | \n", "4882 | \n", "{'kmecoval': 1376, 'robertsr': 24, 'lovef': 75... | \n", "371 | \n", "{'robertsr': 18, 'lovef': 220, 'jamasba': 4, '... | \n", "58 | \n", "{'robertsr': 10, 'ranftp': 1, 'heatha': 1, 'lo... | \n", "{'mooree': 2308, 'adamjohn': 1231, 'kmecoval':... | \n", "390 | \n", "241 | \n", "163 | \n", "
4 | \n", "57353 | \n", "4898 | \n", "{'kmecoval': 1054, 'hsuj': 1, 'koppenhaverb': ... | \n", "302 | \n", "{'hsuj': 1, 'robertsr': 13, 'kmecoval': 17, 's... | \n", "24 | \n", "{'robertsr': 7, 'kmecoval': 2, 'meechank': 13,... | \n", "{'adamjohn': 1843, 'sharifin': 1231, 'masoodpa... | \n", "177 | \n", "247 | \n", "101 | \n", "
\n", " | user | \n", "nodes | \n", "presynapses | \n", "postsynapses | \n", "nodes_reviewed | \n", "
---|---|---|---|---|---|
0 | \n", "robertsr | \n", "14527 | \n", "1038 | \n", "481 | \n", "4729 | \n", "
1 | \n", "ranftp | \n", "5927 | \n", "401 | \n", "132 | \n", "0 | \n", "
2 | \n", "kmecoval | \n", "5204 | \n", "87 | \n", "4 | \n", "5177 | \n", "
3 | \n", "hallouc | \n", "4267 | \n", "61 | \n", "11 | \n", "8047 | \n", "
4 | \n", "michaelLingelbach | \n", "4253 | \n", "1 | \n", "0 | \n", "0 | \n", "
\n", " | total | \n", "creation | \n", "edition | \n", "review | \n", "
---|---|---|---|---|
user | \n", "\n", " | \n", " | \n", " | \n", " |
robertsr | \n", "1113 | \n", "690 | \n", "420 | \n", "198 | \n", "
hallouc | \n", "627 | \n", "183 | \n", "180 | \n", "333 | \n", "
koppenhaverb | \n", "378 | \n", "108 | \n", "15 | \n", "144 | \n", "
ranftp | \n", "357 | \n", "219 | \n", "189 | \n", "0 | \n", "
kmecoval | \n", "333 | \n", "147 | \n", "72 | \n", "126 | \n", "
\n", " | total | \n", "creation | \n", "edition | \n", "review | \n", "
---|---|---|---|---|
user | \n", "\n", " | \n", " | \n", " | \n", " |
robertsr | \n", "588 | \n", "249 | \n", "210 | \n", "177 | \n", "
koppenhaverb | \n", "225 | \n", "96 | \n", "9 | \n", "33 | \n", "
lovef | \n", "198 | \n", "0 | \n", "15 | \n", "162 | \n", "
schlegelp | \n", "171 | \n", "27 | \n", "30 | \n", "66 | \n", "
ranftp | \n", "105 | \n", "69 | \n", "39 | \n", "0 | \n", "
\n", " | node_id | \n", "creation_time | \n", "creator | \n", "edition_time | \n", "editor | \n", "reviewers | \n", "review_times | \n", "
---|---|---|---|---|---|---|---|
0 | \n", "331812 | \n", "2015-05-12 12:31:00 | \n", "13 | \n", "2015-10-20 06:44:00 | \n", "13 | \n", "[53, 13] | \n", "[2016-05-03 14:43:00, 2015-05-12 12:32:00] | \n", "
1 | \n", "331813 | \n", "2015-05-12 12:31:00 | \n", "13 | \n", "2015-10-20 06:44:00 | \n", "13 | \n", "[13, 53] | \n", "[2015-05-12 12:32:00, 2016-05-03 14:43:00] | \n", "
2 | \n", "331814 | \n", "2015-05-12 12:31:00 | \n", "13 | \n", "2015-10-20 06:44:00 | \n", "13 | \n", "[13, 53] | \n", "[2015-05-12 12:32:00, 2016-05-03 14:43:00] | \n", "
3 | \n", "331815 | \n", "2015-05-12 12:31:00 | \n", "13 | \n", "2015-10-20 06:44:00 | \n", "13 | \n", "[13, 53] | \n", "[2015-05-12 12:32:00, 2016-05-03 14:43:00] | \n", "
4 | \n", "331816 | \n", "2015-05-12 12:31:00 | \n", "13 | \n", "2015-10-20 06:44:00 | \n", "13 | \n", "[53, 13] | \n", "[2016-05-03 14:43:00, 2015-05-12 12:32:00] | \n", "
\n", " | node_id | \n", "creation_time | \n", "creator | \n", "edition_time | \n", "editor | \n", "reviewers | \n", "review_times | \n", "creator2 | \n", "
---|---|---|---|---|---|---|---|---|
0 | \n", "331812 | \n", "2015-05-12 12:31:00 | \n", "13 | \n", "2015-10-20 06:44:00 | \n", "13 | \n", "[53, 13] | \n", "[2016-05-03 14:43:00, 2015-05-12 12:32:00] | \n", "adesinaa | \n", "
1 | \n", "331813 | \n", "2015-05-12 12:31:00 | \n", "13 | \n", "2015-10-20 06:44:00 | \n", "13 | \n", "[13, 53] | \n", "[2015-05-12 12:32:00, 2016-05-03 14:43:00] | \n", "adesinaa | \n", "
2 | \n", "331814 | \n", "2015-05-12 12:31:00 | \n", "13 | \n", "2015-10-20 06:44:00 | \n", "13 | \n", "[13, 53] | \n", "[2015-05-12 12:32:00, 2016-05-03 14:43:00] | \n", "adesinaa | \n", "
3 | \n", "331815 | \n", "2015-05-12 12:31:00 | \n", "13 | \n", "2015-10-20 06:44:00 | \n", "13 | \n", "[13, 53] | \n", "[2015-05-12 12:32:00, 2016-05-03 14:43:00] | \n", "adesinaa | \n", "
4 | \n", "331816 | \n", "2015-05-12 12:31:00 | \n", "13 | \n", "2015-10-20 06:44:00 | \n", "13 | \n", "[53, 13] | \n", "[2016-05-03 14:43:00, 2015-05-12 12:32:00] | \n", "adesinaa | \n", "
\n", " | nodes | \n", "connectors | \n", "
---|---|---|
robertsr | \n", "5527 | \n", "1091 | \n", "
koppenhaverb | \n", "2847 | \n", "0 | \n", "
ranftp | \n", "2496 | \n", "349 | \n", "
jefferis | \n", "947 | \n", "11 | \n", "
schlegelp | \n", "914 | \n", "333 | \n", "
\n", " | total | \n", "creation | \n", "edition | \n", "review | \n", "
---|---|---|---|---|
user | \n", "\n", " | \n", " | \n", " | \n", " |
robertsr | \n", "168 | \n", "81 | \n", "51 | \n", "9 | \n", "
schlegelp | \n", "30 | \n", "9 | \n", "9 | \n", "9 | \n", "
alij | \n", "6 | \n", "0 | \n", "0 | \n", "0 | \n", "
sharifin | \n", "6 | \n", "0 | \n", "3 | \n", "0 | \n", "
edmondsona | \n", "6 | \n", "3 | \n", "3 | \n", "0 | \n", "