DOI: 10.5281/zenodo.18672975
title: Chronic two-photon calcium imaging of hippocampal astrocytes, pyramidal cells and interneurons during natural arousal and optogenetic stimulation of locus coeruleus

description: Dataset documentation: Hippocampal neuron and astrocyte responses to noradrenaline and natural aorusal

Overview

This repository contains three MATLAB datasets comprising calcium imaging recordings, behavioral measurements, and locus coeruleus (LC) stimulation responses across multiple experimental conditions and cell types:





Pyramidal neuronsFile:2024-Oct-24_pyramidals_all_datasets_pwcorr_movMod_LC_linear_model_LC_LC.matVariable: pyromice_sian_batch2




AstrocytesFile:2024-Nov-26_astrocytes_all_datasets_pwcorr_movMod_LC_linear_model_LC_LC_activity_bouts.matVariable: astromice_sian_batch2




InterneuronsFile:2025-Sept-23_interneurons_all_datasets_pwcorr_movMod_LC_linear_model_LC_LC_states.matVariable: intermice_sian_batch2



Each dataset consists of a MATLAB cell array where each element corresponds to one imaging session. Sessions include awake behavior or anesthesia.

Datasets were recording using two-photon calcium imaging, with behavioral measurements of pupil diameter, paw movement, and mouth movement using a synchronized video camera, and with recorded time points of behavioral events or optogenetic stimulation of the locus coeruleus (LC).

Session identity is encoded in sessionID, e.g., B1, B2 for awake Behavior, A1 for Anesthesia, and P1 for Pharmacology during anesthesia.

Dataset content

Each .mat file contains one cell array: <celltype>mice_sian_batch2(n)
, where n = number of sessions.

Each session contains the following categories of variables:

1. Session metadata








Variable
Description




sessionID
Unique session identifier (mouse and condition)


parent_folder
Root directory of raw data


frame_rate
Imaging frame rate (Hz)


Meta_data
ScanImage metadata string (raw acquisition parameters)






2. Neural activity variables








Variable
Dimensions
Description




somata_dFF
[T × N]
ΔF/F calcium signal for N ROIs over T timepoints


FOV_dFF
 
Field-of-view averaged ΔF/F


noise_levels
[N × 1]
ROI noise metric


noise_level_accept
[N × 1 logical]
ROI inclusion flag






3. ROI metadata








Variable
Description




ROIs_somata
ROI masks


ROI_somata_ID
ROI identifiers


plane_somata_ID
Imaging plane ID per ROI


anatomy_all
Anatomical reference images (average fluorescence)






4. Behavioral variables








Variable
Dimensions
Description




pupil
[T × 1]
Pupil diameter trace


paw_movement
[T × 1]
Paw movement signal


mouth_movement
[T × 1]
Mouth movement signal






5. LC stimulation variables








Variable
Dimensions
Description




opto_timepoints
[K × 1]
LC stimulation onset in seconds


opto_type_all
[K × 1]
Stimulation type (5 Hz, 20 Hz, 40 Hz, ...)


LC_stimulation_response_dFF
[W × N × K]
Stimulus-triggered ΔF/F


LC_stimulation_response_dFF_normalized
[W × N × K]
Normalized response






Where T = total frames, N = number of ROIs, K = number of stimulation trials, and W = time window around stimulation.

6. Pairwise correlation & spatial metrics








Variable
Description




Pair_wise_correlations
ROI–ROI Pearson correlations


Pair_wise_correlations_wo_LC
Correlations excluding LC-stimulation window times


Pair_wise_correlations_only_LC
Correlations within LC-stimulation window times


Pair_wise_distances
2D ROI distances


Pair_wise_distances_3D
3D ROI distances


Pair_wise_distances_across_planes_only
Cross-plane distances






6. Behavioral modulation analysis

Cross-correlation functions [N × lag_window] and modulation strength [N × 1] of neural activity with body/paw movement or with pupil diameter.

Variables include:

modulation_behavior_xcorr_movement_wo_LC

modulation_behavior_movement_wo_LC

Analogous variables exist for pupil modulation.

 

7. LC modulation indices








Variable
Description




LC_modulation_slow
Slow LC modulation (0-10 s after start of LC stimulation)


LC_modulation_fast
Fast LC modulation (10-20 s after start of LC stimulation)






 

 

Differences Between the Three Datasets








Dataset
Cell type
Special analysis




Pyramidals
Excitatory neurons (CaMKIIa promoter)
ROIs detected with Suite2p; Spike inference of dF/F using Cascade (https://www.nature.com/articles/s41593-021-00895-5; https://www.biorxiv.org/content/10.1101/2025.03.03.641129v3)


Astrocytes
Astrocytes (hGFAP promoter fragment)
Manual selection of ROIs; three imaging planes, spaced by 40 um each


Interneurons
Inhibitory neurons (Dlx promoter)
Manual selection of ROIs; four imaging planes, spaced by 40 um each






 

Suggested Citation

Please cite the associated manuscript (Duss et al., bioRxiv, 2026; https://doi.org/10.64898/2026.01.16.699885) or future peer-reviewed versions of this manuscript, and reference this Zenodo record DOI.