# Data and code availability — Department of Neurophysiology, Kobe University

Where the data and code behind each paper can be found, as stated in the article itself. Last updated: 2026-10-16. 30 entries from 18 papers. Papers not listed here either do not name a public repository or have bibliographic data only in these files. Machine-readable version: https://www.med.kobe-u.ac.jp/neurophy/ai/data.json

## Sound Exposure During Sleep (SES) in PTSD Patients: An Open-Label Feasibility Study (2026)

Paper page: https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ino-2026-medrxiv.md · DOI: 10.64898/2026.05.02.26352243

- data: no link given — “Source data underlying main and supplementary figures are provided as Source Data files, excluding direct personal identifiers”
- code: no link given — “no custom analytical code beyond standard library function calls was required”

## Transient reactivation of small ensembles of adult-born neurons during REM sleep supports memory consolidation in mice (2025)

Paper page: https://www.med.kobe-u.ac.jp/neurophy/ai/papers/srinivasan-2025-nat-commun.md · DOI: 10.1038/s41467-025-62554-8

- data: Mendeley Data — https://doi.org/10.17632/2xfktwhj8x.1 — “Data for LFP and phase-specific silencing study is available at Mendeley Data”
- code: GitHub — https://github.com/vergaloy/Srinivasan_Koyanagi_2025 — “The datasets and custom code used to perform the non-trivial quantitative analyses are available on GitHub”
- code: Zenodo — https://zenodo.org/records/15803872 — “A preserved snapshot of the code at the time of publication has also been archived on Zenodo”

## REM sleep rhythm impairment in people with PTSD (2025)

Paper page: https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sekiba-2025-medrxiv.md · DOI: 10.1101/2025.07.02.25330609

- code: GitHub — https://github.com/seki-haru/PTSD_Sleep_Analysis.git — “Custom MATLAB scripts used for sleep parameter analysis ... are available on GitHub”
- data: (link not given here: not publicly resolvable as of 2026-10-16) — “The data supporting the plots in this study are available on Mendeley Data”

## Memory processing by hippocampal adult-born neurons (2025)

Paper page: https://www.med.kobe-u.ac.jp/neurophy/ai/papers/chavan-2025-neurobiol-learn-mem.md · DOI: 10.1016/j.nlm.2025.108062

- data: no link given — “No data was used for the research described in the article.”

## A comprehensive suite for extracting neuron signals across multiple sessions in one-photon calcium imaging (2025)

Paper page: https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2025-natcommun.md · DOI: 10.1038/s41467-025-58817-z

- data: Dryad — https://doi.org/10.5061/dryad.crjdfn3ck — “Ca2+ imaging videos, simulation code, and additional source data ... are available on Dryad”
- code: GitHub — https://github.com/CaliAli-PV/CaliAli — “The source code for CaliAli, along with demo videos and tutorials, is available on GitHub”
- code: Zenodo — https://doi.org/10.5281/zenodo.14934924 — “A preserved version of the code at the time of publication has been archived on Zenodo”

## T-scope V4: miniaturized microscope for optogenetic tagging in freely behaving animals (2024)

Paper page: https://www.med.kobe-u.ac.jp/neurophy/ai/papers/wang-2024-biorxiv.md · DOI: 10.1101/2024.10.07.616920

- data: Mendeley Data — https://doi.org/10.17632/5g8xf7jgwm.1 — (this DOI did not resolve on 2026-10-16) — “Source data is available at Mendeley Data (DOI: 10.17632/5g8xf7jgwm.1)”

## A pontine-medullary loop crucial for REM sleep and its deficit in Parkinson’s disease (2024)

Paper page: https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kashiwagi-2024-cell.md · DOI: 10.1016/j.cell.2024.08.046

- data: Mendeley Data — https://doi.org/10.17632/46jxff7z75.1 — (this DOI did not resolve on 2026-10-16) — “All raw data analyzed in this paper have been deposited at Mendeley”
- code: no link given — “This paper does not report original code.”

## Distinct ventral hippocampal inhibitory microcircuits regulating anxiety and fear behaviors (2024)

Paper page: https://www.med.kobe-u.ac.jp/neurophy/ai/papers/li-2024-natcommun.md · DOI: 10.1038/s41467-024-52466-4

- data: figshare — https://doi.org/10.6084/m9.figshare.26575084 — “The original data used in this study are available in Figshare repository under open access licence CC BY 4.0.”
- code: figshare — https://doi.org/10.6084/m9.figshare.26575084 — “The Matlab code for AUC analysis used in this study is deposited in Figshare”

## CaliAli, a tool for long-term tracking of neuronal population dynamics in calcium imaging (2023)

Paper page: https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2023-biorxiv.md · DOI: 10.1101/2023.05.19.540935

- code: GitHub — https://github.com/CaliAli-PV/CaliAli — “The codes for CaliAli, along with demo videos and tutorials, are available on GitHub”

## Fully automatic REM sleep stage-specific intervention systems using single EEG in mice (2023)

Paper page: https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyanagi-2023-neurosci-res.md · DOI: 10.1016/j.neures.2022.10.001

- data: no link given — “Data will be made available on Mendeley Data.”

## Open-Source Software for Real-time Calcium Imaging and Synchronized Neuron Firing Detection (2021)

Paper page: https://www.med.kobe-u.ac.jp/neurophy/ai/papers/taniguchi-2021-embc.md · DOI: 10.1109/embc46164.2021.9629611

- code: GitHub — https://github.com/tan1p0p/carignan — “The entire code of the system is available as an open-source software”

## Real-time, automatic, open-source sleep stage classification system using single EEG for mice (2021)

Paper page: https://www.med.kobe-u.ac.jp/neurophy/ai/papers/tezuka-2021-scirep.md · DOI: 10.1038/s41598-021-90332-1

- data: Mendeley Data — https://doi.org/10.17632/5wtxz793my.1 — “Data underlying the results described in this manuscript are available at ... https://doi.org/10.17632/5wtxz793my.1 (after acceptance)”
- data: (link not given here: not publicly resolvable as of 2026-10-16) — “the raw EEG and EMG recording data with stage labels”
- code: GitHub — https://github.com/tarotez/sleepstages — “Code for UTSN and UTSN-L are available at https://github.com/tarotez/sleepstages.”

## Remapping of Adult-Born Neuron Activity during Fear Memory Consolidation in Mice (2021)

Paper page: https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2021-ijms.md · DOI: 10.3390/ijms22062874

- data_and_code: GitHub — https://github.com/vergaloy/Remapping_ABNs — “The data (raw calcium transients and activity traces) and the code supporting the finding of this study (MATLAB) are available”

## Calcium imaging of adult-born neurons in freely moving mice (2021)

Paper page: https://www.med.kobe-u.ac.jp/neurophy/ai/papers/carrier-ruiz-2021-star-protocols.md · DOI: 10.1016/j.xpro.2020.100238

- code: GitHub — https://github.com/vergaloy/ABNs-Calcium-extraction — “Data and code underlying the results described in this manuscript are available at”
- data: Mendeley Data — https://data.mendeley.com/datasets/gfbdv5kfrz/1 — “the raw data from the related article (Kumar et al., 2020) are available at”

## Metabolic fingerprints of fear memory consolidation during sleep (2021)

Paper page: https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyanagi-2021-molbrain.md · DOI: 10.1186/s13041-021-00733-6

- data: Mendeley Data — https://doi.org/10.17632/f6pbcvvbxb.1 — “Data underlying the results described in this manuscript are available at Mendeley Data”

## Sparse Activity of Hippocampal Adult-Born Neurons during REM Sleep Is Necessary for Memory Consolidation (2020)

Paper page: https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kumar-2020-neuron.md · DOI: 10.1016/j.neuron.2020.05.008

- data: Mendeley Data — https://doi.org/10.17632/gfbdv5kfrz.1 — “Data underlying the results described in this manuscript, except raw data for RNA analysis, are available at Mendeley Data”
- data: Mendeley Data — https://doi.org/10.17632/pfgkv43yn7.1 — “RNaseq raw data are available at Mendeley Data”

## Miniaturized microscope with flexible light source input for neuronal imaging and manipulation in freely behaving animals (2019)

Paper page: https://www.med.kobe-u.ac.jp/neurophy/ai/papers/srinivasan-2019-bbrc.md · DOI: 10.1016/j.bbrc.2019.07.082

- design_files: no link given — “The CAD files for the modified housing are available as supplemental files”

## Inhibiting the Activity of CA1 Hippocampal Neurons Prevents the Recall of Contextual Fear Memory in Inducible ArchT Transgenic Mice (2015)

Paper page: https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2015-plos-one.md · DOI: 10.1371/journal.pone.0130163

- data: no link given — “All relevant data are within the paper.”

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Prepared by the Department of Neurophysiology, Kobe University Graduate School of Medicine. Quantitative statements were checked against the published articles.