# Downloading/Accessing Electrophysiology Data for Lee et al., 2023 **URL:** \ **Category:** Technical\ **Tags:** nwb, electrophysiology, allensdk\ **Created:** [October 20, 2023, 9:37pm UTC](https://community.brain-map.org/t/downloading-accessing-electrophysiology-data-for-lee-et-al-2023/2658 "2023-10-20T21:37:14Z")\ **Posts on this page:** 11\ **Page:** 1
**Author:** ![Veritatem\_Amo](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/veritatem_amo/32/420_2.png) [@Veritatem\_Amo](https://community.brain-map.org/u/Veritatem_Amo)\ **Post date:** [October 20, 2023, 9:37pm UTC](https://community.brain-map.org/t/downloading-accessing-electrophysiology-data-for-lee-et-al-2023/2658/1 "2023-10-20T21:37:14Z")
There is a [new paper published this year](https://doi.org/10.1126/science.adf6484), and I have found the [SWC files for morphologies on GitHub](https://github.com/AllenInstitute/human_patchseq_gaba/blob/main/data/LeeDalley_morpho_features.csv). But I cannot find a way to access the electrophysiology sweeps (I used to access the Cell Type Database with AllenSDK, but I assume I can figure something out if someone can point me to the NWB files for the new study as well). I am interested in finding out the stimulus duration and number of spikes for the sweep right above rheobase for each neuron (the “representative sweep”). ---
**Author:** ![brian\_lee](https://avatars.discourse-cdn.com/v4/letter/b/90ced4/32.png) [@brian\_lee](https://community.brain-map.org/u/brian_lee)\ **Post date:** [October 30, 2023, 3:35am UTC](https://community.brain-map.org/t/downloading-accessing-electrophysiology-data-for-lee-et-al-2023/2658/2 "2023-10-30T03:35:34Z")
Hi, thank you for your interest in the paper. The nwb files can be found on DANDI ([DANDI Archive](https://dandiarchive.org/dandiset/000636)). We also have a github location for our data ([GitHub - AllenInstitute/human\_patchseq\_gaba](https://github.com/AllenInstitute/human_patchseq_gaba/tree/main)). Please let me know if you have any additional questions. ---
**Author:** ![Veritatem\_Amo](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/veritatem_amo/32/420_2.png) [@Veritatem\_Amo](https://community.brain-map.org/u/Veritatem_Amo)\ **Post date:** [November 21, 2023, 8:40pm UTC](https://community.brain-map.org/t/downloading-accessing-electrophysiology-data-for-lee-et-al-2023/2658/3 "2023-11-21T20:40:41Z")
Thanks Brian! I checked the DANDI page, where nwb files are group in folders with names like “sub-1000181910”. I assumed that the numeric string after the “sub-” is the specimen ID? However, I cannot find matching IDs with the swc files nor the values in the specimen\_id column of the [LeeDalley\_ephys\_fx.csv](https://github.com/AllenInstitute/human_patchseq_gaba/blob/main/data/LeeDalley_ephys_fx.csv) file on github. How can I get the corresponding nwb files for a given specimen id? ---
**Author:** ![Veritatem\_Amo](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/veritatem_amo/32/420_2.png) [@Veritatem\_Amo](https://community.brain-map.org/u/Veritatem_Amo)\ **Post date:** [November 23, 2023, 12:52am UTC](https://community.brain-map.org/t/downloading-accessing-electrophysiology-data-for-lee-et-al-2023/2658/4 "2023-11-23T00:52:44Z")
Additionally, for each nwb file, when I open them in HDFview, I see the “subject\_id” under “subject”, but no cell IDs/specimen IDs. ---
**Author:** ![Veritatem\_Amo](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/veritatem_amo/32/420_2.png) [@Veritatem\_Amo](https://community.brain-map.org/u/Veritatem_Amo)\ **Post date:** [November 28, 2023, 2:07pm UTC](https://community.brain-map.org/t/downloading-accessing-electrophysiology-data-for-lee-et-al-2023/2658/5 "2023-11-28T14:07:16Z")
@brian_lee Sorry, replied to myself instead of replying to you. ---
**Author:** ![Veritatem\_Amo](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/veritatem_amo/32/420_2.png) [@Veritatem\_Amo](https://community.brain-map.org/u/Veritatem_Amo)\ **Post date:** [November 28, 2023, 7:29pm UTC](https://community.brain-map.org/t/downloading-accessing-electrophysiology-data-for-lee-et-al-2023/2658/6 "2023-11-28T19:29:55Z")
With the [supplied asset file on DANDI](https://api.dandiarchive.org/api/dandisets/000636/versions/draft/assets/), it also does not list the specimen IDs. In the original Allen Cell Type Database, there is a json file for all cells that looks like this that does include a “specimen\_\_id” for each cell (I am including only one cell here): `[{ "cell_reporter_status": null, "csl __normalized_depth": null, "csl__ x": 273.0, "csl __y": 354.0, "csl__ z": 216.0, "donor __age": "25 yrs", "donor__ disease_state": "epilepsy", "donor __id": 524848408, "donor__ name": "H16.03.003", "donor __race": "White or Caucasian", "donor__ sex": "Male", "donor __species": "Homo Sapiens", "donor__ years_of_seizure_history": "9", "ef __adaptation": 0.0278459596639436, "ef__ avg_firing_rate": 13.5725111407696, "ef __avg_isi": 73.6783333333333, "ef__ f_i_curve_slope": 0.1671875, "ef __fast_trough_v_long_square": -53.8750038146973, "ef__ peak_t_ramp": 4.10410666666667, "ef __ri": 159.531131386757, "ef__ tau": 21.1810256736186, "ef __threshold_i_long_square": 90.0, "ef__ upstroke_downstroke_ratio_long_square": 2.89546090494073, "ef __vrest": -70.56103515625, "ephys_inst_thresh_thumb_path": "/api/v2/well_known_file_download/529903142", "ephys_thumb_path": "/api/v2/well_known_file_download/529903140", "erwkf__ id": 618211597, "line_name": "", "m __biophys": 0, "m__ biophys_all_active": 0, "m __biophys_perisomatic": 0, "m__ glif": 5, "morph_thumb_path": null, "nr __average_contraction": null, "nr__ average_parent_daughter_ratio": null, "nr __max_euclidean_distance": null, "nr__ number_bifurcations": null, "nr __number_stems": null, "nr__ reconstruction_type": null, "nrwkf __id": null, "si__ height": null, "si __path": null, "si__ width": null, "specimen __hemisphere": "right", "specimen__ id": 525011903, "specimen __name": "H16.03.003.01.14.02", "structure__ acronym": "FroL", "structure __id": 12113, "structure__ layer": "3", "structure __name": "\"frontal lobe\"", "structure_parent__ acronym": "FroL", "structure_parent __id": 12113, "tag__ apical": "intact", "tag__dendrite_type": "spiny" },...]` ---
**Author:** ![brian\_lee](https://avatars.discourse-cdn.com/v4/letter/b/90ced4/32.png) [@brian\_lee](https://community.brain-map.org/u/brian_lee)\ **Post date:** [November 28, 2023, 8:00pm UTC](https://community.brain-map.org/t/downloading-accessing-electrophysiology-data-for-lee-et-al-2023/2658/7 "2023-11-28T20:00:37Z")
hi @Veritatem_Amo, I have added a new metadata file to our github page (LeeDalley\_manuscript\_metadata\_v2.csv). This sheet has the NWB file name which you will be able to associate the files from the DANDI link. > > > //github.com/AllenInstitute/human\_patchseq\_gaba/tree/main/data ---
**Author:** ![Veritatem\_Amo](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/veritatem_amo/32/420_2.png) [@Veritatem\_Amo](https://community.brain-map.org/u/Veritatem_Amo)\ **Post date:** [November 29, 2023, 7:23pm UTC](https://community.brain-map.org/t/downloading-accessing-electrophysiology-data-for-lee-et-al-2023/2658/8 "2023-11-29T19:23:08Z")
Thank you very much! This is exactly what I need! @brian_lee Just to make sure before I start my downstream analysis, there are about 16 NWB files from DANDI that do not have a specimen ID based on the metadata file. Also, there are 44 NWB IDs from the metadata file that does not have a NWB file from DANDI. Does this sound about right? ---
**Author:** ![Veritatem\_Amo](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/veritatem_amo/32/420_2.png) [@Veritatem\_Amo](https://community.brain-map.org/u/Veritatem_Amo)\ **Post date:** [November 30, 2023, 7:43pm UTC](https://community.brain-map.org/t/downloading-accessing-electrophysiology-data-for-lee-et-al-2023/2658/9 "2023-11-30T19:43:43Z")
@brian_lee One additional question, in the [metadata for electrophysiology](https://github.com/AllenInstitute/human_patchseq_gaba/blob/main/data/LeeDalley_ephys_fx.csv), is “v\_baseline” the resting membrane potential? To my understanding, “rheo” in the column names is short for rheobase; what is “hero” in the column names? ---
**Author:** ![brian\_lee](https://avatars.discourse-cdn.com/v4/letter/b/90ced4/32.png) [@brian\_lee](https://community.brain-map.org/u/brian_lee)\ **Post date:** [December 13, 2023, 4:20am UTC](https://community.brain-map.org/t/downloading-accessing-electrophysiology-data-for-lee-et-al-2023/2658/10 "2023-12-13T04:20:10Z")
Yes v\_baseline is resting membrane potential and rheo is short for rheobase. Hero refers to a suprathreshold voltage trace that contains spiking. ---
**Author:** ![Veritatem\_Amo](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/veritatem_amo/32/420_2.png) [@Veritatem\_Amo](https://community.brain-map.org/u/Veritatem_Amo)\ **Post date:** [January 2, 2024, 2:19am UTC](https://community.brain-map.org/t/downloading-accessing-electrophysiology-data-for-lee-et-al-2023/2658/11 "2024-01-02T02:19:39Z")
Hi @brian_lee, For the morphology of a lot of the neurons from [Brain Image Library,](https://download.brainimagelibrary.org/group/20230426/swc/) there are two SWC files, one ends with “\_transformed.swc”, the other ends with “\_raw.swc”. In some cases, instead of a “\_transformed.swc” file, there is a “\_upright.swc” file. Sometimes there is a single file ending with "\_m.swc. What are the distinctions in between? If I want to model surface area in μm², for instance, which file should I use (right now \_transformed.swc files and \_raw.swc files of the same cell give different numbers)? Thanks and happy new year!