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‎README.md‎

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**Python Module**: Python 3.10 or higher, Python 3.12 recommended
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## Installation, documentation and examples
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https://docs.internationalbrainlab.org
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Installation: https://docs.internationalbrainlab.org/02_installation.html
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Documentation and examples: https://docs.internationalbrainlab.org
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## Contribution and development practices
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See https://int-brain-lab.github.io/iblenv/07_contribution.html
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See https://docs.internationalbrainlab.org/09_contribution.html
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We use Semantic Versioning.
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- run tests `python -m unittest discover`
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Pull request to `develop` or `main`.
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## Matlab Library
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The Matlab library has moved to its own repository here: https://github.com/int-brain-lab/ibllib-matlab/

‎examples/data_release/2025_data_release_autism_noel.md‎

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We recommend you download the data via ONE.
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## Overview of the Data
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We have released data from 198 Neuropixel experimental sessions, with single Neuropixel recordings, referred to as probe insertions. Those were obtained with 62 genetically modified subjects performing the IBL task.
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As output of spike-sorting, there are 71,067 units; of which 12,163 are passing IBL automated quality control.
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We have released data from 364 Neuropixel recordings, referred to as probe insertions. Those were obtained with 62 genetically modified subjects performing the IBL task.
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As output of spike-sorting, there are 129,313 units; of which 22,008 are passing IBL automated quality control.
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| Strain | Subject Count | Recording Count | Units Count | Good Units Count |
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|:---------|--------------:|----------------:|------------:|-----------------:|
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| Cntnap2 | 17 | 52 | 20,467 | 2683 |
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| Fmr1 | 15 | 54 | 17,801 | 3491 |
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| Shank3t | 15 | 41 | 16,357 | 2911 |
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| Wildtype | 15 | 51 | 16,442 | 3078 |
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| Total | 62 | 198 | 71,067 | 12,163 |
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| strain | n_subjects | n_recordings | n_units | n_good_units |
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|:---------|-------------:|-------------:|--------:|-------------:|
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| Cntnap2 | 16 | 85 | 31,082 | 4,211 |
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| Fmr1 | 15 | 105 | 34,401 | 6,215 |
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| Shank3t | 16 | 75 | 31,679 | 5,423 |
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| Wildtype | 15 | 99 | 32,151 | 6,159 |
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| Total | 62 | 364 | 129,313 | 22,008 |
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## Data structure and download
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The organisation of the data follows the standard IBL data structure.
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Please see
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Here is a minimal example of how to download the data for one of the insertions using `ibllib`
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```python
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import pandas as pd
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from brainbox.io.one import SpikeSortingLoader, SessionLoader
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from one.api import ONE
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one = ONE(base_url='https://openalyx.internationalbrainlab.org')
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insertions = one.search_insertions(project='angelaki_mouseASD')
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ssl = SpikeSortingLoader(one=one, pid=str(insertions[0]))
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sl = SessionLoader(one=one, eid=ssl.eid)
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sl.load_trials()
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spikes, clusters, channels = ssl.load_spike_sorting()
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df_clusters = pd.DataFrame(ssl.merge_clusters(spikes, clusters, channels))
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print(df_clusters)
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print(sl.trials)
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```
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To go further with more advanced examples, see:
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* [These instructions](https://int-brain-lab.github.io/iblenv/notebooks_external/data_structure.html) to download an example dataset for one session, and get familiarised with the data structure
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* [These instructions](https://int-brain-lab.github.io/iblenv/notebooks_external/data_download.html) to learn how to use the ONE-api to search and download the released datasets
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Note:
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* The tag associated to this release is `2025_Q3_Noel_et_al_Autism`
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* The project associated to this release is `angelaki_mouseASD`
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## How to cite this dataset
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If you are using this dataset for your research please cite:
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#### Excluded sessions
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The following sessions were excluded as the synchronisation stream from the bpod couldn't be found in the FPGA. As such the behaviour information couldn't be extracted to a clock synced to the electrophysiology.
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| EID | Subject | Date | Number |
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| --- | --- | --- | --- |
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| 5d4e158b-7d6d-48fd-ad94-74ad4704e89f | CSP018 | 2021-01-20 | 001 |
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| 8507e9f6-4da3-454a-b553-3fc8f6299bbb | SH014 | 2020-07-13 | 001 |
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| e9620e9a-688a-45da-ba6e-33fce6753729 | SH008 | 2020-03-04 | 001 |
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| 429de7e8-1fc9-4aa2-87a1-0800268935d7 | CSP023 | 2020-11-17 | 001 |
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11 sessions were excluded as the synchronisation stream from the bpod couldn't be found in the FPGA. As such the behaviour information couldn't be extracted to a clock synced to the electrophysiology.
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#### Video data: QC report
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We have only included video data where we could confidently align the frames timing to the main experiment clock.
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#### Electrophysiology: QC report
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##### Quality of uppermost channels
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What we believe to be a failing Neuropixel headstage translates in the loss of 10-15 of the uppermost channels of the probes. This affects many recordings.
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Make sure to perform an anomaly detection using [ibl-neuropixel](https://github.com/int-brain-lab/ibl-neuropixel) or [spike interface](https://spikeinterface.readthedocs.io/en/stable/)
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##### CRITICAL: Missing spike sorting
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The following insertions do not have any spike sorting available.
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| PID | EID | Subject | Date | Number | Probe |
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| --- | --- | --- | --- | --- | --- |
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| bcb1dac7-6d2b-47ad-bbbe-a4aaf9774481 | b33a5ab8-7b51-4fe4-9ee2-584fb430b41b | FMR025 | 2021-09-02 | 001 | probe01 |
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| a25d9370-a714-4662-88c5-ccf69b646bd5 | 1a4479ec-8511-48c9-9169-55a20f2626f9 | FMR031 | 2022-03-22 | 001 | probe01 |
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| 7bf6ff8d-6487-481e-a174-d1cbe31db2c4 | baab8aae-273e-4f83-80a9-81e9b7f99185 | FMR032 | 2022-03-15 | 001 | probe01 |
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| 65c6349d-6ec3-4a7d-aefc-7cfe328c1faf | 2fe8aa16-faab-49e3-8e13-aceb0b095a30 | SH006 | 2020-02-26 | 001 | probe00 |
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| 7b00f29f-f67f-4fa9-b4c9-e844c44b7b6b | ccffff9f-c432-4377-b228-e2710bc109b6 | SH011 | 2020-02-06 | 001 | probe01 |
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| 8ade2696-5a06-4e0e-8f73-674aaf60a6ca | 8658a5ad-58ce-4626-8d46-be68cd33581b | SH011 | 2020-02-07 | 001 | probe01 |
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| 1606f00b-e4a0-434e-a81b-a492016b42d9 | 792fe5db-dd66-4fc7-ab96-accfce28b7f4 | SH025 | 2022-02-01 | 002 | probe00 |
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| 2a32115c-bb3e-42ec-81a4-c24f11d1721f | 68c22775-1b40-44ff-8802-b95d0152d565 | SH025 | 2022-02-02 | 001 | probe01 |
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| 474965f4-5751-497b-9423-cb130fc30644 | 2d792481-75e5-4e51-a189-20e7cbbcd8ad | SH025 | 2022-02-04 | 002 | probe00 |
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| de7639c4-0f81-4370-84f2-70dde255eca7 | ae21bab0-65dc-40a2-bc6d-48a6a07e9c82 | SH027 | 2022-01-27 | 001 | probe01 |
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| 1034a9c5-85cd-49c1-bf6b-0fb2cbc4ee67 | 576de022-4a2b-4423-8f7f-53f83b1b896e | CSP003 | 2019-11-22 | 001 | probe01 |
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| ef8eb985-3731-48c5-ac62-38214f8d8ee4 | 95fa5278-3870-4087-9c7d-a306a068d334 | CSP031 | 2022-02-01 | 001 | probe01 |
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| eddf08b2-2b1f-489c-bceb-f28592518f61 | bf708a95-5980-463d-b54f-329b49754313 | CSP032 | 2022-01-27 | 001 | probe00 |
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| c31e3510-cc05-4992-ac30-808d3b3f0d81 | d133df68-dec9-4979-a500-a549719424d1 | CSP032 | 2022-01-28 | 001 | probe00 |
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| 131716c1-515e-4a45-9158-cf1af6da39c7 | 86bef629-a95d-4a68-890b-2f7cabb58504 | NYU-57 | 2021-11-18 | 001 | probe00 |
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##### CRITICAL: Missing Histology tracing
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| PID | EID | Subject | Date | Number | Probe |
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| --- | --- | --- | --- | --- | --- |
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| 7d475dc7-a60e-4418-837d-fa9c43a91cff | fb5831ac-d15b-437b-98fe-47d03d7edc15 | SH002 | 2019-11-25 | 001 | probe01 |
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| 2fe497f6-95e8-4349-9b92-47f26265b784 | 0c2f24d9-5184-43e6-97dc-17b31cb8cee9 | SH004 | 2020-02-10 | 002 | probe00 |
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| ada946d0-1195-4f04-9d45-8e7e6adf7f60 | cdfb4449-30fb-4dd9-85cd-c8dd385ddf75 | SH013 | 2020-07-23 | 001 | probe00 |
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| 2eeeee9a-678e-47c9-b2d9-22daec55ddbb | b73a16d7-555d-4c51-91a0-611d0ed0a975 | CSP003 | 2019-11-19 | 001 | probe00 |
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| 5831925c-4b27-425f-9b7a-ff8b0691e9f3 | c1f807b4-7538-4f82-a9a6-52d658eb0bd2 | CSP017 | 2020-11-17 | 001 | probe01 |
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| be8f5333-ea97-4a80-8574-ab937b2087cd | 5f1a76fa-a1b6-4140-83f2-e891db4e11a8 | CSP017 | 2020-11-18 | 001 | probe01 |
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| d8ed8bbe-c2fc-46ad-b769-872d326a8179 | 579881ec-e2f8-4079-b109-100e9ddbe8c0 | CSP017 | 2020-11-19 | 001 | probe01 |
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| 553b258e-e21d-48b2-8065-21246c82e51a | 9c257bc7-ac32-4255-bb03-8ff90dfc2547 | CSP017 | 2020-11-20 | 001 | probe00 |
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##### ERROR: Missing alignments
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#### Electrophysiology: QC report.
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364 insertions were retained for the release, 102 were excluded for the reasons below.
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##### CRITICAL: Missing Histology tracing (17 probes)
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The following insertions do not have any tracing available and won't be recoverable.
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##### ERROR: Missing spike sorting (36 probes)
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The following insertions do not have any spike sorting available, they are not part of the current release but may be part of a future release.
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##### ERROR: Missing alignments (49 probes)
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Here we have spike sorting and histology tracing, but the channels haven´t been aligned. We are not releasing those datasets for the time being.
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Those would be good candidates for a future revision if the ephys atlas task force devises a tool to perform automatic alignments.
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| PID | EID | Subject | Date | Number | Probe |
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| 66887465-3ace-43d6-b609-5e5e1878e8bd | 41eaf4a1-62d6-445f-9284-840b082b31da | FMR030 | 2022-03-29 | 001 | probe01 |
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| eacf11c1-47d5-4245-b715-0acc29ccec5c | 77d47a6a-6e05-4e3e-9c85-49a62feada2a | FMR030 | 2022-03-31 | 001 | probe01 |
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| 131e4225-f661-4d2a-9e82-ce5c476ca33c | 813e255f-9958-4faf-939d-4d1fdc6536de | FMR030 | 2022-04-01 | 001 | probe01 |
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| 58c392e4-1a2e-455e-89eb-65a3ceab8093 | 9c09d626-ef3f-4e51-b353-a578531a8a4b | FMR030 | 2022-04-04 | 001 | probe01 |
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| d805f64c-87dc-459c-b23d-8970483c3127 | badc1a08-030c-4144-91f4-d002a05b6d1f | SH020 | 2021-09-22 | 001 | probe00 |
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| f4fb1053-61a7-482a-9099-39ed436dd756 | 81adee43-8f38-459c-b9ec-f8fee29ddb60 | SH024 | 2021-09-28 | 001 | probe00 |
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| 6f74c301-8d73-49c3-b2fd-6ad1a74528ce | d6492634-aa84-4b51-ab8e-2434648f2d83 | SH024 | 2021-09-29 | 001 | probe00 |
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| af95a0e6-073e-416c-9209-7ab30da8ce02 | 66687fe4-c6f8-40db-96c1-9fc49e07d2b6 | SH024 | 2021-09-30 | 001 | probe00 |
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| 27271de8-f1ff-4299-a547-05f1be477417 | 1862cb56-2241-42c6-9298-a0861d8fb175 | SH024 | 2021-10-01 | 001 | probe00 |
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| 685fb0f1-ed10-4a8b-8e10-51b42a7d67eb | 54859a45-23eb-41ed-b0dc-aa6d6607f006 | SH026 | 2022-03-01 | 001 | probe01 |
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| fcdc2472-1025-41ef-bc0f-2c026c35dd6e | a152d17b-b1e3-4994-89a0-86edbf28661e | SH026 | 2022-03-02 | 001 | probe01 |
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| 94d1359a-3e87-40a5-b747-7e2b85a4330a | 340a0f2b-0201-4c8b-a491-57b8b6320498 | SH026 | 2022-03-03 | 001 | probe01 |
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| 2793cec9-4422-47b4-a58c-4dc5a71baa41 | 7b8d00bf-d7d9-43a4-8f69-50217cfb284c | SH026 | 2022-03-04 | 001 | probe01 |
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| 9dd7e4a7-391a-4f61-982f-0efa470ccf59 | fdd79794-88ea-4a9c-910b-524c150dec48 | CSP001 | 2019-11-20 | 001 | probe00 |
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| 326c22d1-dbce-41dd-92f7-26d6e4a8d9dc | 147d9be2-ab3a-4dd6-a9b8-fdf6fc129d84 | CSP003 | 2019-11-21 | 002 | probe00 |
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| a6b0d2db-c3fc-4967-bdbf-e3f338f3af5e | 9b304cf6-a878-4539-bfd0-aeebcf07f8d1 | CSP023 | 2020-11-18 | 001 | probe01 |
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| c9eb42ff-3d53-4044-9468-93e89d870368 | 9854d7b0-ab63-48d5-a7d6-6b5bf0cf5a30 | CSP026 | 2021-06-08 | 001 | probe00 |
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| 051a6c5f-4a75-42e2-aa82-b4e3cbe1cecf | 26ef4db9-d1b2-4df8-8de7-519accb9883c | CSP026 | 2021-06-09 | 002 | probe00 |
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| 8e5c51e1-690d-4b50-88c4-37242d5ccb65 | 8d3b57dd-4651-4c5f-a4c3-8de8865fdca3 | CSP026 | 2021-06-10 | 001 | probe00 |
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| fab06f3a-9ff5-405d-957c-6e628c25af3d | 7b3be2f3-e11c-4352-b73f-10e7813ccec9 | CSP026 | 2021-06-11 | 001 | probe00 |
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| 8d6c9ffc-6606-4f11-89bf-cc422ce5022a | 50911ee6-732b-4b07-afe0-8c48a287c803 | NYU-49 | 2021-07-23 | 001 | probe01 |

‎examples/exploring_data/data_download.ipynb‎

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{
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"cell_type": "markdown",
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"metadata": {},
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"source": "## Setting up credentials"
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"source": [
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"## Setting up credentials"
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]
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},
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{
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"cell_type": "code",

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