Update brainstem_api_tutorial_new.ipynb

Author: MingzeDou

brainstem_api_tutorial_new.ipynb

@@ -18,7 +18,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -80,28 +80,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Found 18 public projects\n",
-      "\n",
-      "Sample public projects:\n",
-      "1. interaction of acetylcholine and oxytocin neuromodulation in the hippocampus\n",
-      "   Description: <p>A postulated role of subcortical neuromodulators is to control brain states. Mechanisms by which ...\n",
-      "\n",
-      "2. Lore's first project\n",
-      "   Description: <p>Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labo...\n",
-      "\n",
-      "3. Metal microdrive and head cap system for silicon probe recovery in freely moving rodent\n",
-      "   Description: <p>High-yield electrophysiological extracellular recording in freely moving rodents provides a uniqu...\n",
-      "\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# Load public projects (no authentication needed)\n",
     "public_projects = client.load_model(\"project\", portal=\"public\").json()\n",
@@ -163,22 +144,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Found 1 projects matching 'Allen'\n",
-      "Found 1 projects matching all criteria\n",
-      "\n",
-      "Response type: <class 'dict'>\n",
-      "Response contains 'projects' key with data\n",
-      "The id of project is df3c7a20-c03e-48fc-a65d-613cdf1deff9 and the name is Allen Institute: Visual Coding – Neuropixels\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# Basic filtering example\n",
     "filtered_projects = client.load_model(\n",
@@ -221,17 +189,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "{'id': 'df3c7a20-c03e-48fc-a65d-613cdf1deff9', 'name': 'Allen Institute: Visual Coding – Neuropixels', 'description': '<p>The Visual Coding &ndash; Neuropixels project uses high-density extracellular electrophysiology (<strong>Ecephys</strong>) probes to record spikes from a wide variety of regions in the mouse brain. Our experiments are designed to study the activity of the visual cortex and thalamus in the context of passive visual stimulation, but these data can be used to address a wide variety of topics. Allen Brain Observatory Neuropixels dataset; &copy;2019 Allen Institute for Brain Science <a href=\"https://allensdk.readthedocs.io/en/latest/visual_coding_neuropixels.html\">https://allensdk.readthedocs.io/en/latest/visual_coding_neuropixels.html</a></p>', 'sessions': ['6a9c60e9-9a34-4da7-94bc-5bc9da15256f', '017b9289-26f6-4c28-be84-aee554125cd0', '8bab81b4-c37a-445a-b58c-08a19da1479a', '4454e33a-fe89-4745-9e57-9ff5fe561211', 'a452cd24-4b1a-472d-8790-286653e9932f', '857b4729-86ff-4bb1-a439-ea8b4de0207f', '2b2857e5-efd5-40ac-8b09-e994f323e6b4', '24bc997f-9c0f-48a6-9208-b92afaf41070', 'e08859e9-e9d2-456b-b575-312fed608db2', '9fe8d7ab-89c8-4342-96fa-28fc6ea42a1f', '7b2879b2-c84f-4b8b-ac19-84530e4c6937', '6312934d-4410-4b98-a0ab-f2bbdb213772', 'afc9bb52-1b18-4f1e-9907-8163abc3a35e', '6ee69e33-53d1-4250-a31b-988874bd538b', 'af9df978-f79c-4c08-a7a0-d8f47f1356e7', '522bb59f-33a3-46ee-9a27-18b07671dd54', '59eb87c4-eab7-4460-93af-be3859bdb7da', '2c4c4ab0-33c3-430b-9bc9-9644cc38e0d6', 'a3c400ba-7dfd-4a6d-8187-bd2b11f9f775', '2cde90e2-ed9c-43b0-8913-f4abbeacb3e9', 'ecebee2a-9134-42f4-9df2-703703bddd47', '91cc71cc-d049-4b07-840b-840cd250945d', '78d91009-8027-46fb-a0be-03ffb3e0eda1', 'a640c4af-8afb-4c90-a506-94538b31621e', '95463ffb-7b6b-45fa-9d18-408de7c12173', '011025d5-37f2-4f81-ac50-53a10934e55e', 'd230e6f0-35e8-4428-8ec1-a651ac766feb', '5867209b-c483-4a08-9135-d6b6aadf075e', '198f8063-2cd0-46a7-bbea-6633a96f01d8', 'efc517bc-3376-4c2c-8ae9-a3d7fc947144', '3ef8276d-431d-415d-ab65-ef4a3438dd94', '02b0c98f-2a19-48d2-9d53-d786afc3693f', 'e227e74a-4491-420e-925b-0520a3aabcd8', '03baec8f-c8c1-4f70-8c08-d31f72a0922a', '2aeea5e2-6b7e-405f-accb-06775e3f2381', 'c0681602-a36e-4879-8335-3302ffb28ffd', 'f729c943-0d25-47b5-b458-ce6861c7c2fc', '95c7f858-55dd-42dc-8136-a9dcb2ed0d5d', 'bf663b28-9207-4529-8ba1-c44c4166ea67', 'df4edea0-92bc-414a-8133-8ed73e474e21', '071a8ba1-f8e5-4142-a5b4-4848cdec0642', 'b3a4e592-22d1-4a45-80c6-cf7d71c7d6c0', '6e4df6c3-cecc-4db2-a1a3-0f47d195f432', '8d25da3b-e50b-4df4-a524-d3d911e39eed', '044e0b1e-f6b1-4b33-b04d-01e1a98e4405', 'dfb85cae-6335-45c2-9c0e-79eb4907e25e', 'd8ee74dd-0ccc-4d42-89fd-58a4fc231380', 'cb21c91c-db2a-4d54-8d7e-14f9dc6813f5', 'f4be01a2-b767-4cf6-8018-570e09539b2a', '4afd3205-9e2f-4697-8bcc-9a4d2232240f', '3a0babfa-41d4-49e3-bf3a-3c268b1cfc13', '3898e6fa-6b9f-4c45-a8c9-1cb6f227fedd', '2b3f16e9-33f1-4766-88bd-7d23ed2b2861', '40dc0f2f-6e42-4258-b0be-c14b3d535426', '7ccbd85a-90dd-43ee-8683-3437d1873679', '38b8bd8a-42fc-4784-a0a0-d8a0c1b3ae7f', 'f254bdf5-791c-4a0c-8d3b-8b3f4ebcccfb', '366fc12d-b7a2-46ad-8616-900204b092d5'], 'subjects': ['5c786545-ac38-4400-8aac-ef6c60632c91', 'c3e9d58e-501f-4654-b8a4-b3c3be9bbc68', '72c39529-e603-47d6-a5e6-8e71d08f21f1', '4d9849b4-54d9-4044-b10c-9fc2a578cf48', 'e7cbf83a-955a-42e9-ac97-aae99ea5f1e6', '6d350d7e-7fed-47cf-b9cc-e1dd131a86db', 'dc546cb5-e8bf-4886-8cd7-b80baa2fd784', '2db5b7a2-d999-432f-8b87-60d5e70703e3', '7f3abea7-4ffc-41cb-80fa-c83e7d1d2576', '06da91b0-1272-42c0-ac96-2306f8d8d3f3', '62a44cc4-a9d2-44db-9a4e-ec85472fccce', '0e367a33-4349-4be2-8e10-4dec8c774aff', 'e948e72f-1f6e-4aca-b7fe-2276bf7f5757', 'e88691f1-5fc2-4ad0-98c2-2fb3668e3543', 'b0d6abab-ab6c-42c6-8961-46b7c8cafc75', '9cb374be-a6c8-4e38-bf58-59450c27ae5b', 'bad3cde0-1015-4ad6-b202-c0b53e96544b', '8b46b557-dbff-42a0-b1b2-e06795be656a', '8b24e4ce-0f92-4d3a-abf5-e67fc3c1e823', '5724b4cd-27a0-443e-9518-9e2ecc467746', '24f4d844-9835-4a30-8446-e4451247d5c3', '247beab4-b54a-4f9a-8646-2659ce1e606a', '412d86b1-d628-4014-a32f-220ebd3ca0ca', 'ae52cad6-0640-4c88-b92c-19304039370f', 'd3d9e26c-7535-4678-a18c-13b05ad0a38b', '2e58fce9-546f-4594-8cdd-a43dd015fbbe', 'c31258d8-747f-4ff8-9580-d01f74129256', 'df1a8894-018c-45ff-9e31-0e09138e54b2', '82d351fe-91fa-47f5-9ee4-4baa8f50ce8b', '231b0d07-2720-4d1a-b9dc-57cea3c1947f', 'c1f4f28a-0305-4cd9-82d4-4d0577332369', '2a23fe11-7578-4717-9581-ab08c5637d39', 'ec726b09-b385-450a-9929-d5c7e3dfabea', '80948357-c8f6-4458-9610-af1284c9a683', 'b787c935-c978-4a03-8467-ca139add9f65', '23031c50-9abe-48a6-906f-dfbf21b73f8a', 'c7b4458e-7a25-49b1-91c9-8d6f4959afe9', 'a7455a4f-8682-4885-ab93-0c8203c72ea6', '457a8c04-d51f-4559-a2db-6f3d054d813b', 'dc1ed083-cd2b-4f3b-84a9-6c9343fca5e3', 'b9552325-f4c0-4eae-b002-158511d86ab1', 'ef29ca62-7702-4606-8cb9-78888d656d1d', '3c8fc915-09a9-4e7e-a673-b9c21f04ccd2', '85a2953e-0a69-46ca-b28f-ed995e73953f', 'c98211c3-e977-465f-ba98-875da12939ec', 'c55bcca4-316b-4562-8d0c-ccebee0b534c', '26f5152a-d476-4f6f-ba77-4716ddafc44a', '0b7d450a-b5ec-463f-8e11-3f6deabd0126', 'e02dc1ea-3594-463d-af4f-998d5518fcbc', '7d50b5f2-2a89-49a7-9659-6c5b8ed22b74', 'f61c79a1-8c54-4d48-baf4-c38961482c3c', '1a7b9b08-eb53-4f8b-a1df-69cfd490e4de', '2733ecc6-d810-4a34-9bbf-450a4164675e', '81577690-a361-43a3-bc63-0f8c2115880e', 'beb0ad6c-ccb8-461f-bf29-7ed01b185629', '8cd73b74-134b-43cb-b7ad-13a31df1525f', '4b2ff049-338b-4e8a-a087-94404679c01a', 'b36a7385-d935-4df6-b979-2015eeccb9cd'], 'publications': [], 'extra_fields': [], 'is_public': True, 'collections': [], 'cohorts': [], 'tags': [], 'users': {'petersen.peter@gmail.com': {'can_change': True, 'is_manager': True, 'is_owner': True}}, 'groups': {'Buzsaki Lab - NYU': {'can_change': False, 'is_manager': False, 'is_owner': False}}, 'links': {'sessions': 'sessions/', 'subjects': 'subjects/'}}\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "allen_projects = client.load_model(\n",
     "    \"project\", \n",
@@ -243,25 +203,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Project name: Allen Institute: Visual Coding – Neuropixels\n",
-      "Description: <p>The Visual Coding &ndash; Neuropixels project uses high-density extracellular electrophysiology (<strong>Ecephys</strong>) probes to record spikes from a wide variety of regions in the mouse brain....\n",
-      "\n",
-      "This project has 58 subjects\n",
-      "This project has 58 sessions\n",
-      "\n",
-      "Example session details:\n",
-      "ID: 6a9c60e9-9a34-4da7-94bc-5bc9da15256f\n",
-      "Name: session_798911424\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# Find the Allen Institute: Visual Coding – Neuropixels project\n",
     "allen_projects = client.load_model(\n",
@@ -328,41 +272,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Project name: Allen Institute: Visual Coding – Neuropixels\n",
-      "Description: <p>The Visual Coding &ndash; Neuropixels project uses high-density extracellular electrophysiology (...\n",
-      "Public: True\n",
-      "\n",
-      "This project has 58 sessions\n",
-      "This project has 58 subjects\n",
-      "\n",
-      "First 3 subjects in the project:\n",
-      "1. Subject ID: 5c786545-ac38-4400-8aac-ef6c60632c91\n",
-      "2. Subject ID: c3e9d58e-501f-4654-b8a4-b3c3be9bbc68\n",
-      "3. Subject ID: 72c39529-e603-47d6-a5e6-8e71d08f21f1\n",
-      "\n",
-      "First 3 sessions in the project:\n",
-      "1. Session ID: 6a9c60e9-9a34-4da7-94bc-5bc9da15256f\n",
-      "2. Session ID: 017b9289-26f6-4c28-be84-aee554125cd0\n",
-      "3. Session ID: 8bab81b4-c37a-445a-b58c-08a19da1479a\n",
-      "\n",
-      "Session details:\n",
-      "Name: session_798911424\n",
-      "Description: <p>brain_observatory_1.1</p>\n",
-      "\n",
-      "This session has 1 data acquisition method(s) (included in response)\n",
-      "\n",
-      "Data acquisition IDs from session include:\n",
-      "1. 65d48097-cd83-4dfb-a8a1-b8f150ba85c7\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# Find the Allen Institute: Visual Coding – Neuropixels project\n",
     "allen_projects = client.load_model(\n",
@@ -440,26 +352,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "Alphabetically sorted projects:\n",
-      "1. Allen Institute: Visual Coding – Neuropixels\n",
-      "2. CRCNS Frontal cortex: fcx-1\n",
-      "3. CRCNS Hippocampus: hc-1\n",
-      "\n",
-      "Reverse alphabetically sorted projects:\n",
-      "1. Theta rhythm perturbation by focal cooling of the septal pacemaker in awake rats\n",
-      "2. Physiological Properties and Behavioral Correlates of Hippocampal Granule Cells and Mossy Cells\n",
-      "3. Nick Steinmetz Neuropixel data\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# Sort projects alphabetically by name\n",
     "alpha_projects = client.load_model(\n",