Data Repositories and Code for the different Areas of Research in the Cash lab

In an effort to increase open data access and the open science initiatives as well as increase reproducibility and replicability, we have begun to share deidentified intracranial data in some of the below databases as well as our processing code using the FAIR principles and open source practices. Below, we have begun to list the online locations of data and code shared by the Cash lab as well as links to other possibly useful data repositories relevant to each of the research topics below.

Repositories which contain relevant human intracranial data (some including Cash lab data):

DABI: Data Archive BRAIN Initiative- https://dabi.loni.usc.edu/home
The DANDI Archive- https://gui.dandiarchive.org/#/
DRYAD- https://datadryad.org/stash
EBRAINS- https://ebrains.eu/
Zenodo- https://zenodo.org/
OpenNeuro- https://openneuro.org/
Center for Open Science- https://osf.io/

Useful Protocols and Tools from Cash lab and Collaborators

Modular protocol for reconstructing electrode locations in the human brain using multiple software packages (meant to be accessible to naïve users):
- Protocol: https://www.protocols.io/view/modular-reconstruction-and-co-registration-of-imag-5qpvornedv4o/v2
  - From the paper: Modular pipeline for reconstruction and localization of implanted intracranial ECoG and sEEG electrodes
    https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0287921

SEEGAtlas: A framework for the identification and classification of depth electrodes using clinical images :
- Code: https://github.com/IbisNeuronav/IbisPluginsExtraSEEG
  - From the paper: SEEGAtlas: A framework for the identification and classification of depth electrodes using clinical images
    https://iopscience.iop.org/article/10.1088/1741-2552/acd6bd

Neurophysiology of Epilepsy

Cash lab data: Coming soon!
Cash lab code: Coming soon!

Understanding Human Cognition

Cash lab data:
- Data for the paper: Closed-loop enhancement and neural decoding of cognitive control in humans
  - https://zenodo.org/record/5083120#.YlhxZujMIuV
  - https://zenodo.org/record/5085197#.YlhxY-jMIuV
Useful code developed using Cash lab data:
- Encoding and decoding of hidden cognitive states using state space approaches:
  - https://github.com/TRANSFORM-DBS/Encoder-Decoder-Paper
- COMPASS: an open-source, general-purpose software toolkit for computational psychiatry:
  - https://github.com/Eden-Kramer-Lab/COMPASS
- Code for the paper: Closed-loop enhancement and neural decoding of cognitive control in humans
  - https://github.com/tne-lab/MSIT-Nature-Biomedical-Engineering
  - CLoSES-RT: https://github.com/Center-For-Neurotechnology/CLoSES-RT

Brain-Computer Interface Research

Cash lab data:
- WIA data set: https://dabi.loni.usc.edu/dsi/1U01NS098968
Cash lab code:
- CLoSES- Closed-Loop System for Electrical Stimulation (CLoSES) for use with Real-Time Simulink and MATLAB. As a research tool, CLoSES allows for the direct application and interface with ongoing neural activity through efficient, and informed, neuromodulation through direct electrical stimulation.
  - CLoSES-RT: https://github.com/Center-For-Neurotechnology/CLoSES-RT
  - CLoSES-SEM: https://github.com/Center-For-Neurotechnology/CLoSES-SEM

Neuromodulation of the human brain

Cash lab data:
- Data from our single pulse and train intracranial stimulation data sets: https://dabi.loni.usc.edu/dsi/W4SNQ7HR49RL
  - From these papers:
Cash lab code:
- Code for controlling the Cerestim using Matlab: https://github.com/Center-For-Neurotechnology/CereLAB

Neurotechnology

Cash lab data:
- Neuropixels data- https://datadryad.org/stash/dataset/doi:10.5061/dryad.d2547d840
Cash lab code:
- Neuropixels analysis code- https://github.com/Center-For-Neurotechnology/CorticalNeuropixelProcessingPipeline, also at: DOI: 10.5281/zenodo.5753471
- Detection of Type 2 and 3 events in microelectrode recordings: https://github.com/Center-For-Neurotechnology/LFP-Type2-and-Type3-Detection