2026-10-14T16:01:03Z https://www.scidb.cn/oai

10.57760/sciencedb.nb.00039 2026-09-24T09:34:20Z

2026-09-24 Single-Neuron-Resolution cAMP Dynamics in Mouse Primary Visual Cortex (V1) during Fear Memory Acquisition and Retrieval doi:10.57760/sciencedb.nb.00039 en OverviewWe providet an in vivo dataset of spatiotemporal neuronal cAMP two-photon fluorescence signaling in mouse primary visual cortex (V1) acquired during a 3-day fear-conditioning paradigms. A total of 1,844 neurons were stably tracked throughout the three-day recording period, including 1,023 neurons in the light-cued fear conditioning group (n = 25 mice) and 821 neurons in the contextual fear conditioning group (n = 16 mice). The dataset comprises raw and corrected fluorescence images, Suite2p and Track2p processing outputs, curated single-neuron activity traces, synchronous behavioral videos and freezing behavior scores, event timestamp files, as well as comprehensive metadata and Python analysis workflows.. Task Summary Experimental group 1 (Light-cued fear conditioning) — Day 1 (Pre-test): Mice were placed in fear-conditioning context A. During this time, four non-reinforced blue-light stimuli (5 s each) were delivered with a 90-s inter-stimulus interval. Day 2 (Training): The mice were returned to context A and received four blue-light stimuli (5 s each). These were accompanied by a 1 s foot shock (1 mA) that occurred simultaneously with the final second of each light stimulus. Day 3 (Test): Mice were placed in a novel context B with distinct visual and tactile stimuli and received four non-reinforced blue-light stimuli (5 s each).Experimental group 2 (Contextual fear conditioning) — Day 1 (Training): The mice received four footshocks (1 s each, 0.75 mA) with a 90-s inter-stimulus interval in context A, without a light–shock pairing. Day 2 (Test 1): Mice were re-exposed to context A during which no shock stimuli were applied. Day 3 (Test 2): Mice were exposed to a novel context B without foot-shock stimuli.  Data Preprocessing and Neuron IdentificationRaw two-photon fluorescence images (TIFF format) were processed using a multi-step pipeline: original raw microscope data → mean-projection quality control → SuperNerve motion correction → Fiji-based spatial alignment (XY translation, rotation, and common-field cropping) → independent Suite2p processing of Day 1, Day 2, and Day 3 → Track2p cross-day ROI matching → manual curation. Raw source data and outputs from each processing stage were stored separately to maintain traceability. DataContentFluorescence imaging data — (1) The ‘1_raw_data’ folder contains the original microscope TIFF stacks. (2) The ‘2_suite2p_track2p/<ID>_MCXYdata/dayN/*.tif’ folder contains the quality-screened, motion-corrected, Fiji-aligned, and cropped TIFF stacks for each imaging day. (3) The ‘dayN/suite2p/plane0’ folder contains the Suite2p output for the corresponding session. Detailed documentation of Suite2p output files is available at ‘https://suite2p.readthedocs.io/en/latest/outputs/’. (4) the ‘<ID>_MCXYdata/track2p’ directory stores registration parameters, ROI match matrices, QC figures, and three-day matches (automated and manual) in and ‘curated_matched_suite2p’, respectively.Behavioral video recordings — The ‘6_behavior/Rawdata_Video/Video_<ID>’ directory contains daily behavioral video recordings of individual mice in AVI format. The ‘6_behavior/Data_Freezing/<ID>_Freezing.xlsx’ file contains second-by-second binary scores (0 = movement; 1 = freezing) across the three experimental days. Event annotations — ‘4_cue_timeline/<ID>_time_line.csv’ contains frame counting information and session labels for each experimental day. The total number of rows per day matches the exact number of acquired fluorescence frames. The paired ‘<ID>_cue.csv’ documents the daily session tags and light cue timestamps that mark the four stimulus onsets per day that are registered to the fluorescence-frame timeline.Fluorescence data preprocessing and analysis outputs — The ‘3_Preprocessing_analysis’ directory contains results from manually curated three-day matched neuronal at the mouse and group levels. The mouse-specific folders provide neuronal x–y coordinates, quality control and photobleaching reports, corrected fluorescence traces, event-aligned dF/F and Z-score traces, AUC-/s-based response classifications, and heatmaps. The ‘Summary’ directory contains group-level z-score and AUC/s tables. The z-score traces are interpolated to a common time axis from −20-s to +60-s at 8.65 Hz. The ’Output’ subdirectory contains response-state transition tables, alluvial and donut plots, and the corresponding chi-square or Fisher's exact test results.Analysis code — The customized Python scripts in the ‘5_code’ folder implement a standardized, sequential analytical workflow: neuropil/QC/bleaching correction; cue-aligned dF/F, Z-score, AUC metrics, and activity heatmap; extraction of curated cell coordinates; cross-session merging and signal interpolation at the group level; visualization and statistical evaluation of neuronal activity state transitions. Additional utility scripts enable the batch processing of all curated mouse datasets, the automated construction and validation of project manifests and the conversion of curated NumPy arrays to CSV files. Conda environment files and package-version records are included for Track2p and statistical analysis.Metadata and navigation — The ‘20260904_twophoton_data_v2.xlsx’ file contains information on individual mouse IDs, experimental group assignments, imaging frame rates, single-day neuronal cell counts, and neuronal matching statistics derived from automatic three-day registration and final manual curation. The ‘project_data_manifest.csv’ file contains a catalog of each unique mouse-day session in individual rows, establishing standardized relative file paths that link corrected TIFF stacks, Suite2p processing outputs, Track2p cross-day matching results, cue/timeline files, and analysis results. The ‘software_versions.csv’ file lists the verified software and package versions. cAMP; primary visual cortex (V1); fear conditioning; two-photon imaging Yuan Li Yuanyao Yang Xing Liu Qiumin Le Lan Ma Fan Wang Feifei Wang EMBARGO https://creativecommons.org/licenses/by/4.0/ dataset Science Data Bank