Chronic two-photon calcium imaging of hippocampal astrocytes, pyramidal cells and interneurons during natural arousal and optogenetic stimulation of locus coeruleus

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.