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README.md

Code repository for Hasegawa & Huang et al.

This code can be used to generate main and supplementary figures of Hasegawa, Huang, Paricio-Montesinos & Gründemann (original preprint https://doi.org/10.1101/2023.08.23.554119).

Data can be downloaded from the data repository https://gin.g-node.org/GrundemannLab/2024_Hasegawa_Huang_et_al_DATA.

Code can be executed in MATLAB2020a (MathWorks).

Fig1-2 and Fig S1, 3, 4, 6
Load data by load('...\Fig*\*.mat').

Fig3-4, SVM_decoding
Laod data by load('...\Data\Fig3_FigS7-18\*\*.mat').

Supplementary figures S7-S18
Figures can be generated with the code from the main figures (see annotations).

Load helper functions by running addpath(genpath('...\auxillary'));

Data structure:
'DataAll.(Aud1)': Initial auditory-go group
'DataAll.(Vis1)': Initial visual-go group
E.g. DataAll.('Aud1')(n).BHV.Naive{m}.FieldName (n: n-th mouse; m: m-th session)

FieldName
StimStart: Stimulus start time (s)
ICF: raw calcium trace (sample,cell)
LickPulse: Lick time (s)
Trial_Freq: Auditory stimulus frequency
Trial_Grat: Visual stimulus angle
RotaryEncPulse: Rotary encoder pulse (no direction)

datacite.yml
Title Code for: Network state changes in sensory thalamus represent learned outcomes
Authors Hasegawa,Masashi;German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany and University of Basel, Department of Biomedicine, Basel, Switzerland
Huang,Ziyan;German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
Paricio-Montesinos,Ricardo;German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
Gründemann,Jan;German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany and University of Basel, Department of Biomedicine, Basel, Switzerland
Description Code for generation of figures of Hasegawa, Huang, Paricio-Montesinos, Gründemann, 2024. Network state changes in sensory thalamus represent learned outcome. Code can be used to perform single cell and poplulation level analyses of in vivo calcium imaging data from mice.
License BSD 3-Clause License (https://opensource.org/license/bsd-3-clause)
References Hasegawa M, Huang Z, Paricio-Montesinos R, Gründemann J (2024) Network state changes in sensory thalamus represent learned outcomes. tba [doi:tba] (IsSupplementTo)
Hasegawa M, Huang Z, Paricio-Montesinos R, Gründemann J (2024) Data for: Network state changes in sensory thalamus represent learned outcomes. G-Node. https://doi.org/10.12751/g-node.7xxnmw [doi:10.12751/g-node.7xxnmw] (IsReferencedBy)
Funding DFG; SFB1089, SPP2411, Walter Benjamin Programme 528405672
EU; ERC Starting Grant 803870
Swiss National Science Foundation; PP00P3_170672
Schweizerische Hirnliga; Forschungspreis
The Forschungsfonds Nachwuchsforschende of the University of Basel
The Department of Biomedicine at the University of Basel
Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE)
DZNE Innovative Minds Program
Keywords Neuroscience
Thalamus
Imaging
Resource Type Software