GrundemannLab/2024_Hasegawa_Huang_et_al_CODE

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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

README.md

Code repository for Hasegawa & Huang et al.