{
  "generated": "2026-10-16",
  "schema_version": "1.0",
  "description": "Data and code availability as stated in each article.",
  "count": 30,
  "entries": [
    {
      "paper_id": "ino-2026-medrxiv",
      "doi": "10.64898/2026.05.02.26352243",
      "year": 2026,
      "title": "Sound Exposure During Sleep (SES) in PTSD Patients: An Open-Label Feasibility Study",
      "type": "data",
      "url": null,
      "repository": null,
      "as_stated": "Source data underlying main and supplementary figures are provided as Source Data files, excluding direct personal identifiers",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ino-2026-medrxiv.md"
    },
    {
      "paper_id": "ino-2026-medrxiv",
      "doi": "10.64898/2026.05.02.26352243",
      "year": 2026,
      "title": "Sound Exposure During Sleep (SES) in PTSD Patients: An Open-Label Feasibility Study",
      "type": "code",
      "url": null,
      "repository": null,
      "as_stated": "no custom analytical code beyond standard library function calls was required",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/ino-2026-medrxiv.md"
    },
    {
      "paper_id": "srinivasan-2025-nat-commun",
      "doi": "10.1038/s41467-025-62554-8",
      "year": 2025,
      "title": "Transient reactivation of small ensembles of adult-born neurons during REM sleep supports memory consolidation in mice",
      "type": "data",
      "url": "https://doi.org/10.17632/2xfktwhj8x.1",
      "repository": "Mendeley Data",
      "as_stated": "Data for LFP and phase-specific silencing study is available at Mendeley Data",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/srinivasan-2025-nat-commun.md"
    },
    {
      "paper_id": "srinivasan-2025-nat-commun",
      "doi": "10.1038/s41467-025-62554-8",
      "year": 2025,
      "title": "Transient reactivation of small ensembles of adult-born neurons during REM sleep supports memory consolidation in mice",
      "type": "code",
      "url": "https://github.com/vergaloy/Srinivasan_Koyanagi_2025",
      "repository": "GitHub",
      "as_stated": "The datasets and custom code used to perform the non-trivial quantitative analyses are available on GitHub",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/srinivasan-2025-nat-commun.md"
    },
    {
      "paper_id": "srinivasan-2025-nat-commun",
      "doi": "10.1038/s41467-025-62554-8",
      "year": 2025,
      "title": "Transient reactivation of small ensembles of adult-born neurons during REM sleep supports memory consolidation in mice",
      "type": "code",
      "url": "https://zenodo.org/records/15803872",
      "repository": "Zenodo",
      "as_stated": "A preserved snapshot of the code at the time of publication has also been archived on Zenodo",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/srinivasan-2025-nat-commun.md"
    },
    {
      "paper_id": "sekiba-2025-medrxiv",
      "doi": "10.1101/2025.07.02.25330609",
      "year": 2025,
      "title": "REM sleep rhythm impairment in people with PTSD",
      "type": "code",
      "url": "https://github.com/seki-haru/PTSD_Sleep_Analysis.git",
      "repository": "GitHub",
      "as_stated": "Custom MATLAB scripts used for sleep parameter analysis ... are available on GitHub",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sekiba-2025-medrxiv.md"
    },
    {
      "paper_id": "sekiba-2025-medrxiv",
      "doi": "10.1101/2025.07.02.25330609",
      "year": 2025,
      "title": "REM sleep rhythm impairment in people with PTSD",
      "type": "data",
      "url": null,
      "repository": null,
      "status": "not_publicly_resolvable_2026-10-16",
      "as_stated": "The data supporting the plots in this study are available on Mendeley Data",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sekiba-2025-medrxiv.md"
    },
    {
      "paper_id": "chavan-2025-neurobiol-learn-mem",
      "doi": "10.1016/j.nlm.2025.108062",
      "year": 2025,
      "title": "Memory processing by hippocampal adult-born neurons",
      "type": "data",
      "url": null,
      "repository": null,
      "as_stated": "No data was used for the research described in the article.",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/chavan-2025-neurobiol-learn-mem.md"
    },
    {
      "paper_id": "vergara-2025-natcommun",
      "doi": "10.1038/s41467-025-58817-z",
      "year": 2025,
      "title": "A comprehensive suite for extracting neuron signals across multiple sessions in one-photon calcium imaging",
      "type": "data",
      "url": "https://doi.org/10.5061/dryad.crjdfn3ck",
      "repository": "Dryad",
      "as_stated": "Ca2+ imaging videos, simulation code, and additional source data ... are available on Dryad",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2025-natcommun.md"
    },
    {
      "paper_id": "vergara-2025-natcommun",
      "doi": "10.1038/s41467-025-58817-z",
      "year": 2025,
      "title": "A comprehensive suite for extracting neuron signals across multiple sessions in one-photon calcium imaging",
      "type": "code",
      "url": "https://github.com/CaliAli-PV/CaliAli",
      "repository": "GitHub",
      "as_stated": "The source code for CaliAli, along with demo videos and tutorials, is available on GitHub",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2025-natcommun.md"
    },
    {
      "paper_id": "vergara-2025-natcommun",
      "doi": "10.1038/s41467-025-58817-z",
      "year": 2025,
      "title": "A comprehensive suite for extracting neuron signals across multiple sessions in one-photon calcium imaging",
      "type": "code",
      "url": "https://doi.org/10.5281/zenodo.14934924",
      "repository": "Zenodo",
      "as_stated": "A preserved version of the code at the time of publication has been archived on Zenodo",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2025-natcommun.md"
    },
    {
      "paper_id": "wang-2024-biorxiv",
      "doi": "10.1101/2024.10.07.616920",
      "year": 2024,
      "title": "T-scope V4: miniaturized microscope for optogenetic tagging in freely behaving animals",
      "type": "data",
      "url": "https://doi.org/10.17632/5g8xf7jgwm.1",
      "repository": "Mendeley Data",
      "status": "doi_not_resolving_2026-10-16",
      "as_stated": "Source data is available at Mendeley Data (DOI: 10.17632/5g8xf7jgwm.1)",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/wang-2024-biorxiv.md"
    },
    {
      "paper_id": "kashiwagi-2024-cell",
      "doi": "10.1016/j.cell.2024.08.046",
      "year": 2024,
      "title": "A pontine-medullary loop crucial for REM sleep and its deficit in Parkinson’s disease",
      "type": "data",
      "url": "https://doi.org/10.17632/46jxff7z75.1",
      "repository": "Mendeley Data",
      "status": "doi_not_resolving_2026-10-16",
      "as_stated": "All raw data analyzed in this paper have been deposited at Mendeley",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kashiwagi-2024-cell.md"
    },
    {
      "paper_id": "kashiwagi-2024-cell",
      "doi": "10.1016/j.cell.2024.08.046",
      "year": 2024,
      "title": "A pontine-medullary loop crucial for REM sleep and its deficit in Parkinson’s disease",
      "type": "code",
      "url": null,
      "repository": null,
      "as_stated": "This paper does not report original code.",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kashiwagi-2024-cell.md"
    },
    {
      "paper_id": "li-2024-natcommun",
      "doi": "10.1038/s41467-024-52466-4",
      "year": 2024,
      "title": "Distinct ventral hippocampal inhibitory microcircuits regulating anxiety and fear behaviors",
      "type": "data",
      "url": "https://doi.org/10.6084/m9.figshare.26575084",
      "repository": "figshare",
      "as_stated": "The original data used in this study are available in Figshare repository under open access licence CC BY 4.0.",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/li-2024-natcommun.md"
    },
    {
      "paper_id": "li-2024-natcommun",
      "doi": "10.1038/s41467-024-52466-4",
      "year": 2024,
      "title": "Distinct ventral hippocampal inhibitory microcircuits regulating anxiety and fear behaviors",
      "type": "code",
      "url": "https://doi.org/10.6084/m9.figshare.26575084",
      "repository": "figshare",
      "as_stated": "The Matlab code for AUC analysis used in this study is deposited in Figshare",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/li-2024-natcommun.md"
    },
    {
      "paper_id": "vergara-2023-biorxiv",
      "doi": "10.1101/2023.05.19.540935",
      "year": 2023,
      "title": "CaliAli, a tool for long-term tracking of neuronal population dynamics in calcium imaging",
      "type": "code",
      "url": "https://github.com/CaliAli-PV/CaliAli",
      "repository": "GitHub",
      "as_stated": "The codes for CaliAli, along with demo videos and tutorials, are available on GitHub",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2023-biorxiv.md"
    },
    {
      "paper_id": "koyanagi-2023-neurosci-res",
      "doi": "10.1016/j.neures.2022.10.001",
      "year": 2023,
      "title": "Fully automatic REM sleep stage-specific intervention systems using single EEG in mice",
      "type": "data",
      "url": null,
      "repository": null,
      "as_stated": "Data will be made available on Mendeley Data.",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyanagi-2023-neurosci-res.md"
    },
    {
      "paper_id": "taniguchi-2021-embc",
      "doi": "10.1109/embc46164.2021.9629611",
      "year": 2021,
      "title": "Open-Source Software for Real-time Calcium Imaging and Synchronized Neuron Firing Detection",
      "type": "code",
      "url": "https://github.com/tan1p0p/carignan",
      "repository": "GitHub",
      "as_stated": "The entire code of the system is available as an open-source software",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/taniguchi-2021-embc.md"
    },
    {
      "paper_id": "tezuka-2021-scirep",
      "doi": "10.1038/s41598-021-90332-1",
      "year": 2021,
      "title": "Real-time, automatic, open-source sleep stage classification system using single EEG for mice",
      "type": "data",
      "url": "https://doi.org/10.17632/5wtxz793my.1",
      "repository": "Mendeley Data",
      "as_stated": "Data underlying the results described in this manuscript are available at ... https://doi.org/10.17632/5wtxz793my.1 (after acceptance)",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/tezuka-2021-scirep.md"
    },
    {
      "paper_id": "tezuka-2021-scirep",
      "doi": "10.1038/s41598-021-90332-1",
      "year": 2021,
      "title": "Real-time, automatic, open-source sleep stage classification system using single EEG for mice",
      "type": "data",
      "url": null,
      "repository": null,
      "status": "not_publicly_resolvable_2026-10-16",
      "as_stated": "the raw EEG and EMG recording data with stage labels",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/tezuka-2021-scirep.md"
    },
    {
      "paper_id": "tezuka-2021-scirep",
      "doi": "10.1038/s41598-021-90332-1",
      "year": 2021,
      "title": "Real-time, automatic, open-source sleep stage classification system using single EEG for mice",
      "type": "code",
      "url": "https://github.com/tarotez/sleepstages",
      "repository": "GitHub",
      "as_stated": "Code for UTSN and UTSN-L are available at https://github.com/tarotez/sleepstages.",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/tezuka-2021-scirep.md"
    },
    {
      "paper_id": "vergara-2021-ijms",
      "doi": "10.3390/ijms22062874",
      "year": 2021,
      "title": "Remapping of Adult-Born Neuron Activity during Fear Memory Consolidation in Mice",
      "type": "data_and_code",
      "url": "https://github.com/vergaloy/Remapping_ABNs",
      "repository": "GitHub",
      "as_stated": "The data (raw calcium transients and activity traces) and the code supporting the finding of this study (MATLAB) are available",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/vergara-2021-ijms.md"
    },
    {
      "paper_id": "carrier-ruiz-2021-star-protocols",
      "doi": "10.1016/j.xpro.2020.100238",
      "year": 2021,
      "title": "Calcium imaging of adult-born neurons in freely moving mice",
      "type": "code",
      "url": "https://github.com/vergaloy/ABNs-Calcium-extraction",
      "repository": "GitHub",
      "as_stated": "Data and code underlying the results described in this manuscript are available at",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/carrier-ruiz-2021-star-protocols.md"
    },
    {
      "paper_id": "carrier-ruiz-2021-star-protocols",
      "doi": "10.1016/j.xpro.2020.100238",
      "year": 2021,
      "title": "Calcium imaging of adult-born neurons in freely moving mice",
      "type": "data",
      "url": "https://data.mendeley.com/datasets/gfbdv5kfrz/1",
      "repository": "Mendeley Data",
      "as_stated": "the raw data from the related article (Kumar et al., 2020) are available at",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/carrier-ruiz-2021-star-protocols.md"
    },
    {
      "paper_id": "koyanagi-2021-molbrain",
      "doi": "10.1186/s13041-021-00733-6",
      "year": 2021,
      "title": "Metabolic fingerprints of fear memory consolidation during sleep",
      "type": "data",
      "url": "https://doi.org/10.17632/f6pbcvvbxb.1",
      "repository": "Mendeley Data",
      "as_stated": "Data underlying the results described in this manuscript are available at Mendeley Data",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/koyanagi-2021-molbrain.md"
    },
    {
      "paper_id": "kumar-2020-neuron",
      "doi": "10.1016/j.neuron.2020.05.008",
      "year": 2020,
      "title": "Sparse Activity of Hippocampal Adult-Born Neurons during REM Sleep Is Necessary for Memory Consolidation",
      "type": "data",
      "url": "https://doi.org/10.17632/gfbdv5kfrz.1",
      "repository": "Mendeley Data",
      "as_stated": "Data underlying the results described in this manuscript, except raw data for RNA analysis, are available at Mendeley Data",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kumar-2020-neuron.md"
    },
    {
      "paper_id": "kumar-2020-neuron",
      "doi": "10.1016/j.neuron.2020.05.008",
      "year": 2020,
      "title": "Sparse Activity of Hippocampal Adult-Born Neurons during REM Sleep Is Necessary for Memory Consolidation",
      "type": "data",
      "url": "https://doi.org/10.17632/pfgkv43yn7.1",
      "repository": "Mendeley Data",
      "as_stated": "RNaseq raw data are available at Mendeley Data",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/kumar-2020-neuron.md"
    },
    {
      "paper_id": "srinivasan-2019-bbrc",
      "doi": "10.1016/j.bbrc.2019.07.082",
      "year": 2019,
      "title": "Miniaturized microscope with flexible light source input for neuronal imaging and manipulation in freely behaving animals",
      "type": "design_files",
      "url": null,
      "repository": null,
      "as_stated": "The CAD files for the modified housing are available as supplemental files",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/srinivasan-2019-bbrc.md"
    },
    {
      "paper_id": "sakaguchi-2015-plos-one",
      "doi": "10.1371/journal.pone.0130163",
      "year": 2015,
      "title": "Inhibiting the Activity of CA1 Hippocampal Neurons Prevents the Recall of Contextual Fear Memory in Inducible ArchT Transgenic Mice",
      "type": "data",
      "url": null,
      "repository": null,
      "as_stated": "All relevant data are within the paper.",
      "paper_url": "https://www.med.kobe-u.ac.jp/neurophy/ai/papers/sakaguchi-2015-plos-one.md"
    }
  ]
}