Merge remote-tracking branch 'refs/remotes/origin/master'

README.md

@@ -1,14 +1,22 @@
 # Anesthesia_CA1
 
-This repository contains data related to the article "Anesthetics fragment hippocampal network activity, alter spine dynamics and affect memory consolidation" (https://www.biorxiv.org/content/10.1101/2020.06.05.135905v1).
+This repository contains data related to the article "Anesthetics fragment hippocampal network activity, alter spine dynamics and affect memory consolidation" (https://www.biorxiv.org/content/10.1101/2020.06.05.135905v1). Published in PLOS Biology doi: [10.1371/journal.pbio.3001146](https://doi.org/10.1371/journal.pbio.3001146).
+
+We provide calcium imaging and electrophysiology data from hippocampal CA1 during wakefulness, sleep and under various general anesthetics (Isoflurane, Keta/Xyl and MMF).
+
+
+**Awake**             |  **Isoflurane**       |  **Keta/Xyl**   |   **MMF**   
+:-------------------------:|:-------------------------:|:-------------------------:|:-------------------------:
+![](repo_figures/51_awake_256_256.gif)  |  ![](repo_figures/51_iso_256_256.gif) | ![](repo_figures/51_keta_256_256.gif) | ![](repo_figures/51_MMF_256_256.gif) 
 
-We provide calcium imaging and electrophysiology data from hippocampal CA1 during wakefulness, sleep and under various general anesthetics.
 Following the structure of the repository, the dataset contains:
 - LFP and SUA recordings from 4 mice under Isoflurane, Keta/Xyl and MMF anesthesia (electrophysiology folder)
 - 189 distinct 2-photon calcium imaging recordings from 7 different mice under Isoflurane, Keta/Xyl and MMF anesthesia (calcium imaging folder)
 - LFP and SUA recordings in awake and sleep conditions (with sleep scoring) from 7 and 4 mice respectively (Sleep Data/LFP and Sleep Data/SUA folders)
 - 74 distinct 2-photon calcium imaging recordings from 3 mice in awake and sleep conditions (Sleep Data/calcium imaging folder)
 
+This repository contains electrophysiological data and processed calcium imaging recordings. Raw calcium imaging recordings are available in [another repository](https://gin.g-node.org/SW_lab/Calcium_imaging_CA1_raw).
+
 ## Data structure info
 
 Most data structure should be self explanatory / inferrable from the description in the manuscript, but some useful information is provided in the respective "meta_data" excel files.
@@ -18,4 +26,4 @@ Most data structure should be self explanatory / inferrable from the description
 - information about the numpy calcium imaging files can be found in the suite2p documentation page (https://suite2p.readthedocs.io/en/latest/)
 - for LFP data, only the CA1 reversal channel is provided
 - LFP data has a sampling rate of 320 Hz and has been band-pass filtered in the 0.1-160 Hz range
-- code used for analysis/stats and stats dataset can be found at https://github.com/mchini/Yang_Chini_et_al and https://github.com/OpatzLab/HanganuOpatzToolbox
+- code used for the analysis and statistics together with stats-dataset can be found at https://github.com/mchini/Yang_Chini_et_al and https://github.com/OpatzLab/HanganuOpatzToolbox

datacite.yml

@@ -0,0 +1,121 @@
+# Metadata for DOI registration according to DataCite Metadata Schema 4.1.
+# For detailed schema description see https://doi.org/10.5438/0014
+
+## Required fields
+
+# The main researchers involved. Include digital identifier (e.g., ORCID)
+# if possible, including the prefix to indicate its type.
+authors:
+  -
+    firstname: "Andrey"
+    lastname: "Formozov"
+    affiliation: "Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany"
+    id: "ORCID:0000-0001-8935-8612"
+  -
+    firstname: "Mattia"
+    lastname: "Chini"
+    affiliation: "Institute of Developmental Neurophysiology, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany"
+    id: "ORCID:0000-0002-5782-9720"
+  -
+    firstname: "Alexander"
+    lastname: " Dieter"
+    affiliation: "Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany"
+    id: "ORCID:0000-0002-9154-4833"
+  -
+    firstname: "Wei"
+    lastname: "Yang"
+    affiliation: "Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany"
+    id: "ORCID:0000-0002-1052-8808"
+  -
+    firstname: "Jastyn A."
+    lastname: "Pöpplau"
+    affiliation: "Institute of Developmental Neurophysiology, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany"
+    id: "ORCID:0000-0002-4350-3164"
+  -
+    firstname: "Ileana L."
+    lastname: "Hanganu-Opatz"
+    affiliation: "Institute of Developmental Neurophysiology, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany"
+    id: "ORCID:0000-0002-4787-1765"
+  -
+    firstname: "J. Simon"
+    lastname: "Wiegert"
+    affiliation: "Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany"
+    id: "ORCID:0000-0003-0893-9349"
+ 
+
+# A title to describe the published resource.
+title: "Calcium imaging and electrophysiology of hippocampal activity under anesthesia and natural sleep in mice"
+
+
+# Additional information about the resource, e.g., a brief abstract.
+description: |
+  Large-scale, annotated collection of 
+  2-photon calcium imaging
+  data and electrophysiological recordings in CA1 of the murine hippocampus
+  under three distinct anesthetics
+  (Isoflurane, Keta/Xyl and MMF), 
+  during natural sleep, and during wakefulness.
+
+# Lit of keywords the resource should be associated with.
+# Give as many keywords as possible, to make the resource findable.
+keywords:
+  - Neuroscience
+  - Anesthesia
+  - Anaesthesia
+  - Sleep
+  - Recovery
+  - Hippocampus
+  - CA1
+  - Pyramidal neurons
+  - Calcium imaging data
+  - Electrophysiological recordings
+  - Pupillometry
+  - EMG data
+
+# License information for this resource. Please provide the license name and/or a link to the license.
+# Please add also a corresponding LICENSE file to the repository.
+license:
+  name: "Creative Commons CC0 1.0 Public Domain Dedication"
+  url: "https://creativecommons.org/publicdomain/zero/1.0/"
+
+
+## Optional Fields
+
+# Funding information for this resource.
+# Separate funder name and grant number by comma.
+funding:
+  - "German Research Council, SFB936/B8"
+  - "German Research Council, SFB936/B5"
+  - "European Research Council, ERC-2016-StG-714762"
+  - "European Research Council, ERC-2015-CoG-681577 "
+  - "Alexander von Humboldt Foundation, Research Fellowship"
+  - "EU-project euSNN, MSCA-ITN-H2020-860563"
+  - "Landesforschungsförderung Hamburg, LFF76 and LFF73"
+  - "Chinese Scholarship Council, CSC 201606210129"
+
+
+# Related publications. reftype might be: IsSupplementTo, IsDescribedBy, IsReferencedBy.
+# Please provide digital identifier (e.g., DOI) if possible.
+# Add a prefix to the ID, separated by a colon, to indicate the source.
+# Supported sources are: DOI, arXiv, PMID
+# In the citation field, please provide the full reference, including title, authors, journal etc.
+references:
+
+  -
+    reftype: "IsDescribedBy"
+    citation: "Formozov, A. et al. Calcium imaging and electrophysiology of hippocampal activity under anesthesia and natural sleep in mice. Scientific data. 2022"
+
+  -
+    id: "doi:10.1371/journal.pbio.3001146"
+    reftype: "IsSupplementTo"
+    citation: "Yang, W., Chini, M. et al. Anesthetics fragment hippocampal network activity, alter spine dynamics, and affect memory consolidation. PLoS biology, 19(4), e3001146"
+  -
+    id: "doi:10.12751/g-node.s549qk"
+    reftype: "IsDerivedFrom"
+    citation: "Formozov A, Chini M, Dieter A, Yang W, Pöpplau JA, Hanganu-Opatz IL, Wiegert JS (2022) Calcium imaging of hippocampal activity under anesthesia and natural sleep in mice. G-Node. https://doi.org/10.12751/g-node.s549qk"
+
+# Resource type. Default is Dataset, other possible values are Software, DataPaper, Image, Text.
+resourcetype: Dataset
+
+# Do not edit or remove the following line
+templateversion: 1.2