Cell Type Lookup Table Metadata#
import pandas as pd
import numpy as np
from datetime import datetime, date
from aind_data_access_api.document_db import MetadataDbClient
API_GATEWAY_HOST = "api.allenneuraldynamics.org"
DATABASE = 'metadata_index'
COLLECTION = 'data_assets'
docdb_api_client = MetadataDbClient(
host=API_GATEWAY_HOST,
database=DATABASE,
collection=COLLECTION,
)
print(docdb_api_client._base_url)
https://api.allenneuraldynamics.org/v1/metadata_index/data_assets
aggregate = [
{
"$match": {
"data_description.project_name": {"$in": ["Cell Type Lookup Table", "Cell Type LUT"]},
"name": {"$regex": "nwb"},
"location": {"$regex": "aind-open-data"},
"data_description": {"$ne": None}
}
},
{
"$project": {
"name": 1,
"subject_id": "$data_description.subject_id",
"genotype": "$subject.subject_details.genotype",
"date_of_birth": "$subject.subject_details.date_of_birth",
"sex": "$subject.subject_details.sex",
"session_start_time": "$acquisition.acquisition_start_time",
"session_end_time": "$acquisition.acquisition_end_time",
"stimulus_epochs": "$acquisition.stimulus_epochs.stimulus_name",
"project_name": "$data_description.project_name",
"modality": "$data_description.modalities.name",
"virus_names": "$procedures.subject_procedures.procedures.injection_materials.name",
}
},
]
records = docdb_api_client.aggregate_docdb_records(
pipeline=aggregate,
)
Return these records into a dataframe and do some cleanup (exclude a particular session)
to_exclude = ['ecephys_655565_2023-03-31_14-47-36_nwb_2025-07-16_16-52-27']
df = pd.DataFrame(records)
filtered_df = df[~df.name.isin(to_exclude)].sort_values(by='name')
# flatten virus names
filtered_df.virus_names = filtered_df.virus_names.apply(lambda x: [item for sublist in x for item in sublist] if isinstance(x, list) else x)
filtered_df
| _id | name | subject_id | genotype | date_of_birth | sex | session_start_time | session_end_time | stimulus_epochs | project_name | modality | virus_names | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 38 | 63df2bac-e58a-42e8-8edf-799851dee447 | ecephys_655565_2023-04-03_13-34-16_nwb_2025-07... | 655565 | Chat-IRES-Cre-neo/Chat-IRES-Cre-neo | 2022-10-24 | Male | 2023-04-03T20:30:00Z | 2023-04-03T22:30:00Z | [] | Cell Type Lookup Table | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0452h_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 3 | be7e6c7f-c5a2-420e-8b0d-f709353df6f1 | ecephys_655565_2023-04-05_16-17-25_nwb_2025-06... | 655565 | Chat-IRES-Cre-neo/Chat-IRES-Cre-neo | 2022-10-24 | Male | 2023-04-05T16:17:25-07:00 | 2023-04-05T17:05:43-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0452h_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 5 | f8e4c6d5-7176-4f21-9b88-d04238fda04c | ecephys_655568_2023-05-01_15-26-47_nwb_2025-06... | 655568 | Chat-IRES-Cre-neo/Chat-IRES-Cre-neo | 2022-10-24 | Female | 2023-05-01T15:26:47-07:00 | 2023-05-01T16:13:33-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0779m_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 1 | 5826720c-6582-4ea7-94e0-4c9aa4afa7a9 | ecephys_655568_2023-05-03_15-21-12_nwb_2025-06... | 655568 | Chat-IRES-Cre-neo/Chat-IRES-Cre-neo | 2022-10-24 | Female | 2023-05-03T15:21:12-07:00 | 2023-05-03T16:07:54-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0779m_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 4 | cbde19ea-5cde-4a1a-af95-231903f1c6e2 | ecephys_655571_2023-05-09_13-53-48_nwb_2025-06... | 655571 | Chat-IRES-Cre-neo/Chat-IRES-Cre-neo | 2022-10-24 | Female | 2023-05-09T13:53:48-07:00 | 2023-05-09T14:41:36-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0779m_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 0 | 01ecc549-edaf-4594-885d-a12f97e87599 | ecephys_655571_2023-05-15_13-39-49_nwb_2025-06... | 655571 | Chat-IRES-Cre-neo/Chat-IRES-Cre-neo | 2022-10-24 | Female | 2023-05-15T13:39:49-07:00 | 2023-05-15T14:26:36-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0779m_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 2 | 714a99ce-6734-415c-8fa5-287d33a2fd27 | ecephys_655572_2023-05-09_15-03-29_nwb_2025-06... | 655572 | Chat-IRES-Cre-neo/Chat-IRES-Cre-neo | 2022-10-24 | Female | 2023-05-09T15:03:29-07:00 | 2023-05-09T15:51:02-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0779m_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 21 | 4db46f40-57a6-4d37-bff6-eda1f8e09023 | ecephys_655572_2023-05-15_15-06-36_nwb_2025-06... | 655572 | Chat-IRES-Cre-neo/Chat-IRES-Cre-neo | 2022-10-24 | Female | 2023-05-15T15:06:36-07:00 | 2023-05-15T15:53:44-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0779m_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 23 | 9e4044f0-bc26-47cb-9f5d-e605a0076cf4 | ecephys_660104_2023-07-24_18-18-13_nwb_2025-07... | 660104 | Sst-IRES-Cre/wt | 2022-11-30 | Female | 2023-07-24T18:18:13-07:00 | 2023-07-24T19:04:58-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0452h_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 39 | 166a3fda-dee1-47a3-938c-1ee549bc3448 | ecephys_661398_2023-03-31_17-01-09_nwb_2025-07... | 661398 | Adora2a-Cre/wt | 2022-12-10 | Male | 2023-04-01T00:00:00Z | 2023-04-01T02:00:00Z | [] | Cell Type Lookup Table | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0779m_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 40 | 6cd80d0a-0c5b-493c-8783-5b4ec6ca0bd6 | ecephys_661398_2023-04-03_15-47-29_nwb_2025-07... | 661398 | Adora2a-Cre/wt | 2022-12-10 | Male | 2023-04-03T20:30:00Z | 2023-04-03T22:30:00Z | [] | Cell Type Lookup Table | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0779m_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 22 | 96bc69e4-5456-4591-b7c8-cc514ccdcf5b | ecephys_661398_2023-04-06_16-02-15_nwb_2025-06... | 661398 | Adora2a-Cre/wt | 2022-12-10 | Male | 2023-04-06T16:02:15-07:00 | 2023-04-06T16:50:38-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0779m_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 28 | c02a863b-e63e-4f35-9be8-1fd7277cfd96 | ecephys_662913_2023-07-20_16-15-45_nwb_2025-06... | 662913 | Adora2a-Cre/wt | 2022-12-25 | Male | 2023-07-20T16:15:45-07:00 | 2023-07-20T17:02:09-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0779m_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 25 | 0cb30136-5e40-480b-8a8d-d26cea462730 | ecephys_666721_2023-05-09_11-01-03_nwb_2025-06... | 666721 | Drd1a-Cre/wt | 2023-01-24 | Male | 2023-05-09T11:01:03-07:00 | 2023-05-09T11:47:46-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0452h_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 24 | 00b6e0cc-632e-4b71-805a-91c0b312f12d | ecephys_666721_2023-05-12_16-15-36_nwb_2025-06... | 666721 | Drd1a-Cre/wt | 2023-01-24 | Male | 2023-05-12T16:15:36-07:00 | 2023-05-12T17:03:19-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0452h_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 27 | a1a64a17-fa3d-456e-be13-ab4427f14ded | ecephys_666859_2023-06-13_14-19-34_nwb_2025-06... | 666859 | Adora2a-Cre/wt | 2023-01-25 | Female | 2023-06-13T14:19:34-07:00 | 2023-06-13T14:47:34-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0779m_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 26 | 64a5b115-a9a5-4cb9-892d-8af5f875eb81 | ecephys_666861_2023-05-23_10-04-20_nwb_2025-06... | 666861 | Adora2a-Cre/wt | 2023-01-25 | Female | 2023-05-23T10:04:20-07:00 | 2023-05-23T10:49:58-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0779m_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 7 | 9910cc8e-8bf0-4235-bbc8-89536f3d6071 | ecephys_666861_2023-05-24_14-30-05_nwb_2025-06... | 666861 | Adora2a-Cre/wt | 2023-01-25 | Female | 2023-05-24T14:30:05-07:00 | 2023-05-24T15:16:29-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0779m_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 6 | 45cdaffe-3f25-4574-8117-a735e7bdabab | ecephys_671646_2023-07-31_15-21-40_nwb_2025-07... | 671646 | Chat-IRES-Cre-neo/Chat-IRES-Cre-neo | 2023-02-25 | Female | 2023-07-31T15:21:40-07:00 | 2023-07-31T16:13:00-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0452h_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 11 | a647216f-e791-48b9-bb7a-8ac500c7eeeb | ecephys_674005_2023-08-08_15-39-38_nwb_2025-06... | 674005 | Chat-IRES-Cre-neo/Chat-IRES-Cre-neo | 2023-03-14 | Male | 2023-08-08T15:39:38-07:00 | 2023-08-08T16:21:53-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0452h_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 13 | dca6ae43-e43c-4043-9512-38bf07c0f820 | ecephys_674005_2023-08-10_13-15-14_nwb_2025-06... | 674005 | Chat-IRES-Cre-neo/Chat-IRES-Cre-neo | 2023-03-14 | Male | 2023-08-10T13:15:14-07:00 | 2023-08-10T14:18:18-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0452h_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 10 | 41df8893-c20b-427a-94c3-3b1182c916b7 | ecephys_678449_2023-08-28_17-53-41_nwb_2025-07... | 678449 | Gad2-IRES-Cre/Gad2-IRES-Cre | 2023-04-10 | Female | 2023-08-28T17:53:41-07:00 | 2023-08-28T18:28:17-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-Ef1a-DIO-ChRmine-mScarlet-WPRE]] |
| 12 | c398b858-bf4f-4ad9-8204-1079006b5279 | ecephys_678577_2023-11-06_15-58-49_nwb_2025-06... | 678577 | Ntrk1-IRES-Cre/wt | 2023-04-11 | Male | 2023-11-06T15:58:49-08:00 | 2023-11-06T16:40:11-08:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0779m_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 8 | 0094c6ad-50c3-49fd-b5a0-3180d643573a | ecephys_682033_2023-10-26_14-21-51_nwb_2025-07... | 682033 | Gad2-IRES-Cre/Gad2-IRES-Cre | 2023-05-02 | Female | 2023-10-26T14:21:51-07:00 | 2023-10-26T14:56:21-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-Ef1a-DIO-ChRmine-mScarlet-WPRE]] |
| 9 | 2f60b59b-fe68-43ee-a8de-c79002bd8bcf | ecephys_682085_2023-10-03_16-42-49_nwb_2025-07... | 682085 | Slc17a6-IRES-Cre/wt | 2023-05-03 | Male | 2023-10-03T16:42:49-07:00 | 2023-10-03T17:31:24-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-Ef1a-DIO-ChRmine-mScarlet-WPRE]] |
| 29 | 4e2b3d26-4b67-4819-806d-3f55da5929ba | ecephys_684156_2023-10-11_17-45-08_nwb_2025-07... | 684156 | Drd1a-Cre/wt | 2023-05-14 | Female | 2023-10-11T17:45:08-07:00 | 2023-10-11T18:49:28-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0743m_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 30 | fe201555-1613-41d6-90ca-adec417feffe | ecephys_684156_2023-10-13_16-56-59_nwb_2025-07... | 684156 | Drd1a-Cre/wt | 2023-05-14 | Female | 2023-10-12T16:56:59-07:00 | 2023-10-12T18:01:04-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0743m_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 19 | 76119c86-e2bc-4dcb-8654-8405e5ba4fa3 | ecephys_692497_2023-12-11_16-20-55_nwb_2025-07... | 692497 | Adora2a-Cre/wt | 2023-07-06 | Female | 2023-12-11T16:20:55-08:00 | 2023-12-11T17:02:52-08:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[hSyn-DIO-somBiPOLES-mCerulean]] |
| 32 | ca77c9d1-1b23-45c6-b40f-d53e651a59a3 | ecephys_692497_2023-12-15_16-29-04_nwb_2025-07... | 692497 | Adora2a-Cre/wt | 2023-07-06 | Female | 2023-12-15T16:29:04-08:00 | 2023-12-15T17:10:29-08:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[hSyn-DIO-somBiPOLES-mCerulean]] |
| 36 | 2a2f70d3-6b11-4d6b-81e5-ce4c2943a867 | ecephys_694471_2023-12-11_14-51-57_nwb_2025-06... | 694471 | Ntrk1-IRES-Cre/wt | 2023-07-19 | Male | 2023-12-11T14:51:57-08:00 | 2023-12-11T15:33:49-08:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0779m_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 34 | 7d0cfa81-9dde-4f78-a8cd-b35e91b44cc9 | ecephys_694471_2023-12-15_15-26-01_nwb_2025-06... | 694471 | Ntrk1-IRES-Cre/wt | 2023-07-19 | Male | 2023-12-15T15:26:01-08:00 | 2023-12-15T16:07:28-08:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0779m_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 33 | 0ec2e8ae-316d-49e7-91ed-c024dd0ad79c | ecephys_694473_2023-11-28_15-23-23_nwb_2025-07... | 694473 | Ntrk1-IRES-Cre/wt | 2023-07-19 | Female | 2023-11-28T15:23:23-08:00 | 2023-11-28T16:05:02-08:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0779m_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 35 | a0cdab6a-0905-4907-b4d5-2d85bf860b61 | ecephys_697577_2024-02-13_16-24-10_nwb_2025-07... | 697577 | Adora2a-Cre/wt | 2023-08-07 | Male | 2024-02-13T16:24:10-07:00 | 2024-02-13T17:05:24-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology] | [[pAAV-Syn-FLEX-rc(ChrimsonR-tdTomato)]] |
| 20 | 143a7ece-9bbf-42bc-856e-cf6f6c780d57 | ecephys_704242_2024-04-30_17-13-29_nwb_2025-07... | 704242 | Gad2-IRES-Cre/Gad2-IRES-Cre | 2023-09-21 | Male | 2024-04-30T17:13:29-07:00 | 2024-04-30T17:40:53-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-Ef1a-DIO ChRmine-eYFP-WPRE]] |
| 15 | 4eac050d-ab62-47f1-b4f5-c486057f22f2 | ecephys_704242_2024-05-02_16-51-50_nwb_2025-07... | 704242 | Gad2-IRES-Cre/Gad2-IRES-Cre | 2023-09-21 | Male | 2024-05-02T16:51:50-07:00 | 2024-05-02T17:20:47-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-Ef1a-DIO ChRmine-eYFP-WPRE]] |
| 17 | bf0fba2f-94f9-4ae0-8dc1-82776316166d | ecephys_715287_2024-04-24_15-24-43_nwb_2025-07... | 715287 | Ntrk1-IRES-Cre/wt | 2023-12-04 | Female | 2024-04-24T15:24:43-07:00 | 2024-04-24T15:54:45-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0452h_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 18 | c8585e3d-bcf7-4191-ae7e-fa5b0b830fa0 | ecephys_715290_2024-05-09_15-39-23_nwb_2025-07... | 715290 | Ntrk1-IRES-Cre/wt | 2023-12-04 | Female | 2024-05-09T15:39:23-07:00 | 2024-05-09T16:12:34-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0452h_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 16 | 5192c6f9-c327-40fb-a026-d3ef3ec4cc02 | ecephys_715339_2024-05-08_16-09-35_nwb_2025-07... | 715339 | Drd1a-Cre/wt | 2023-12-04 | Female | 2024-05-08T16:09:35-07:00 | 2024-05-08T16:37:43-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0452h_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 31 | 4b3e05be-bdfa-471a-acb6-94316f4d2f9d | ecephys_719093_2024-05-13_16-42-41_nwb_2025-07... | 719093 | Chat-IRES-Cre/Chat-IRES-Cre | 2024-01-02 | Male | 2024-05-13T16:42:41-07:00 | 2024-05-13T17:10:56-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0452h_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
| 14 | 27a5f834-6975-4a6f-b5f7-796074135e77 | ecephys_719093_2024-05-15_15-01-10_nwb_2025-07... | 719093 | Chat-IRES-Cre/Chat-IRES-Cre | 2024-01-02 | Male | 2024-05-15T15:01:10-07:00 | 2024-05-15T15:29:15-07:00 | [Laser pulses] | Cell Type LUT | [Extracellular electrophysiology, Behavior vid... | [[pAAV-AiE0452h_3xC2-minBG-CoChR-EGFP-WPRE3-BG... |
print(len(filtered_df))
40
print(filtered_df.genotype.unique().tolist())
['Chat-IRES-Cre-neo/Chat-IRES-Cre-neo', 'Sst-IRES-Cre/wt', 'Adora2a-Cre/wt', 'Drd1a-Cre/wt', 'Gad2-IRES-Cre/Gad2-IRES-Cre', 'Ntrk1-IRES-Cre/wt', 'Slc17a6-IRES-Cre/wt', 'Chat-IRES-Cre/Chat-IRES-Cre']