2025 - Autism

This is the dataset associated with the publication A common computational and neural anomaly across mouse models of autism.

Electrophysiology, behavioral and video data were collected in mice performing the IBL task. Animals were either wildtype, or from one of 3 different autism models:

  • B6.129P2-Fmr1tm1Cgr/J JAX Strain #003025

  • B6.129(Cg)-Cntnap2tm2Pele/J JAX Strain #028635

  • B6.129-Shank3tm2Gfng/J JAX Strain #017688

The following data repository contains intermediate results and code to reproduce the analysis: https://osf.io/fap2s/ and https://osf.io/fap2s/wiki/home/.

Please note that different quality standards were applied in the article than what is presented in this page. For example, the IBL does not use a presence ratio to assess the quality of its good spike sorting units.

Notes

The dataset has also been published via the OSF platform. However, downloading the dataset through OSF is not recommended. We recommend you download the data via ONE.

Overview of the Data

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. As output of spike-sorting, there are 129,313 units; of which 22,008 are passing IBL automated quality control.

strain

n_subjects

n_recordings

n_units

n_good_units

Cntnap2

16

85

31,082

4,211

Fmr1

15

105

34,401

6,215

Shank3t

16

75

31,679

5,423

Wildtype

15

99

32,151

6,159

Total

62

364

129,313

22,008

Data structure and download

The organisation of the data follows the standard IBL data structure.

Here is a minimal example of how to download the data for one of the insertions using ibllib

import pandas as pd
from brainbox.io.one import SpikeSortingLoader, SessionLoader
from one.api import ONE

one = ONE(base_url='https://openalyx.internationalbrainlab.org')
insertions = one.search_insertions(project='angelaki_mouseASD')
ssl = SpikeSortingLoader(one=one, pid=str(insertions[0]))
sl = SessionLoader(one=one, eid=ssl.eid)
sl.load_trials()
spikes, clusters, channels = ssl.load_spike_sorting()
df_clusters = pd.DataFrame(ssl.merge_clusters(spikes, clusters, channels))
print(df_clusters)
print(sl.trials)

To go further with more advanced examples, see:

  • These instructions to download an example dataset for one session, and get familiarised with the data structure

  • These instructions to learn how to use the ONE-api to search and download the released datasets

  • These instructions to get familiarised with specific data loading functions

Note:

  • The tag associated to this release is 2025_Q3_Noel_et_al_Autism

  • The project associated to this release is angelaki_mouseASD

How to cite this dataset

If you are using this dataset for your research please cite:

Data release notes and changelog

2025-08-29: initial release

Possible future evolutions:

  • Spike sorting re-run with iblsorter or newer algorithm to have better yield and better pre-processing

  • Perfom new alignments of the brain region labels with regards to the ephys signatures using an automatic tool

Excluded sessions

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.

Video data: QC report

We have only included video data where we could confidently align the frames timing to the main experiment clock.

Quality of uppermost channels

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. Make sure to perform an anomaly detection using ibl-neuropixel or spike interface

Electrophysiology: QC report.

364 insertions were retained for the release, 102 were excluded for the reasons below.

CRITICAL: Missing Histology tracing (17 probes)

The following insertions do not have any tracing available and won’t be recoverable.

ERROR: Missing spike sorting (36 probes)

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.

ERROR: Missing alignments (49 probes)

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. Those would be good candidates for a future revision if the ephys atlas task force devises a tool to perform automatic alignments.