11  Course data

This page includes information on the provenance of all data used in the course and instructions on how to download it from open access datasets on DANDI archive and from the International Brain Laboratory (IBL).

Beyond this course, it is a useful to be aware of these excellent resources. They are very valuable for testing pipelines, comparing your datasets to others data collected from the same region or using the same probe. Further, they allow you to perform your own interesting analysis without collecting data. For example, this recent Paninski/Fusi-lab paper was based on their analysis of the International Brain Lab (IBL)’s open Brainwide Map.

12 Head direction experiment from the DANDI archive

Used in preprocessing, sorting, postprocessing and Pynapple analysis.

The DANDI archive is an open, NIH-backed repository for sharing neurophysiology datasets in the standardized Neurodata without borders (NWB) file format (which SpikeInterface can load).

You can explore the many datasets on their website, and download them using the Python API (used in this course) or DANDI’s own command line interface API using the Dandiset ID and the path to the asset you want or DANDI’s own API.

The dataset we will use through the majority of this course is hosted on DANDI here. The data was used in Duszkiewicz et al., 2024. The experiments recorded from the postsubiculum, a parahippocampal cortical region of the parahippocampal formation and a key hub of the spatial navigation system, using a 64-channel single-shank Cambridge Neurotech probe. They recorded from mice using open-field exploration (as well as during sleep) in which they measured the head-direction of the mice. They were interested in investigating neural tuning for head direction (i.e. head-direction tuned neurons fire when the head of an animal is facing a particular direction or angle).

The function found [here] TODO: ADD LINK can be used to download and save datasets (either the entire recording or parts of it) using SpikeInterface. We will use it to download the dataset above, but the same approach works for any of the thousands of recordings hosted on DANDI.

13 IBL Benchmark dataset

Used in Preprocessing (part 1).

The IBL Benchmark dataset is a curated set of 11 Neuropixels recordings in varied brain regions available publicly via the Open Neurophysiology Environment (ONE) API. Data can be streamed directly — no bulk download required.

The script below demonstrates how to: TODO: ADD THIS LINK

  1. Connect to the public IBL server and select a probe insertion by its pid
  2. Stream a short snippet of raw AP-band voltage
  3. Apply a Butterworth high-pass filter (300 Hz) to remove LFP/DC drift
  4. Run the full IBL destriping pipeline (ADC shift correction + spatial k-filter)
  5. Open all three stages side-by-side in the viewephys interactive viewer

TODO: link to the code, will refactor first

14 Introductory dataset

Used in the pipeline walkthrough chapter

TODO: check with Steve and finish section

This dataset is a short 2.5 second period from a BRAIN REGION recording on a 4-shank NP2 probe (NP2010). It uses electrodes on the central two of the four shanks.

This is from a dataset by Steve Lenzi (Margrie Lab) (LINK) from an chronic-recording experiment in which a mouse learnt to suppress escape behavior when presented with an aversive, looming visual stimulus.

This data is included in the course repository here, as it is very small. **TODO: link to set up page (and describe how to manually dl it?)