DOI: 10.57760/sciencedb.35040
title: Awake Mouse Connectome Project (AMCP): Whole-Brain Awake fMRI, DTI, Structural MRI, and Multiphase Behavioral Video Data from 212 Sex-balanced Mice
title: Awake Mouse Connectome Project (AMCP): Whole-Brain Awake fMRI, DTI, Structural MRI, and Multiphase Behavioral Video Data from 212 Sex-balanced Mice

description: This dataset was generated as part of the Awake Mouse Connectome Project (AMCP), which aims to establish a large-scale, standardized resource of awake mouse neuroimaging and behavioral data for investigating whole-brain structure, functional connectivity, and their relationships with behavior under physiologically relevant conditions. The present public release includes data from 212 adult C57BL/6N mice, acquired under fully awake conditions, together with synchronized behavioral video recordings.All mice were 8 weeks of age at the start of the experiments and were purchased one week prior to data collection to allow acclimation to the laboratory environment. Animals were group-housed by sex (no more than five per cage) in individually ventilated cages under a 12-hour light/dark cycle, with controlled temperature and humidity and ad libitum access to food and water. All experimental procedures were conducted under standardized conditions to minimize environmental variability.To enable awake MRI acquisition, each mouse underwent surgical implantation of a custom-made, MRI-compatible head holder. Surgeries were performed under isoflurane anesthesia, with body temperature maintained throughout the procedure. After exposing and cleaning the skull, the head holder was secured using dental adhesive and light-cured dental resin to ensure long-term stability. A transparent dental cement layer was applied to protect the exposed skull and facilitate postoperative monitoring. Postoperative analgesia was administered continuously for one week, followed by a recovery period prior to habituation.After recovery, mice underwent a 14-day habituation protocol designed to acclimate them to head fixation and scanner acoustic noise. During habituation, animals were secured in a custom MRI-compatible animal bed and exposed to recorded MRI sounds with gradually increasing intensity and duration. By the final stage, mice were exposed to sound levels and durations equivalent to those used during actual scanning. No rewards were provided during habituation.MRI data were acquired at Changping Laboratory using a 9.4 Tesla small-animal MRI system(uMR, United Imaging Life Science Instrument, Wuhan, China), equipped with an 86-mm volume transmit coil and a four-channel mouse head surface receive coil. For each mouse, high-resolution T2-weighted structural images, resting-state BOLD functional MRI, and diffusion tensor imaging (DTI) data were collected. T2-weighted images covered the whole brain with a spatial resolution of 0.1 × 0.1 × 0.5 mm³. Resting-state functional MRI was acquired using a gradient-echo EPI sequence under awake conditions, consisting of four runs per animal, each yielding 480 usable volumes after initial dummy scans, for a total of 1920 time points per mouse. The temporal resolution was 1 second, with a voxel size of 0.15 × 0.15 × 0.5 mm³. Field maps and pairs of EPI images with opposite phase-encoding directions were acquired to support correction of susceptibility-induced distortions. DTI data were acquired using a multi-shot diffusion-weighted EPI sequence with isotropic 0.2 mm resolution, including one non-diffusion-weighted volume and 32 diffusion-weighted directions at two b-values (800 and 1600 s/mm²). All MRI data are provided as raw NIfTI files without preprocessing.Within one week following MRI acquisition, all mice underwent a battery of freely moving behavioral tests to ensure temporal proximity between imaging and behavioral assessments. The behavioral assays included the open field test, novel object recognition test, and Y-maze tests assessing spontaneous alternation and novel arm preference. The Y-maze protocol consisted of sequential exploration, familiarization, and recall phases, while the open field and object recognition tasks were conducted in a square arena across multiple phases. All behavioral sessions were video recorded under standardized conditions, with apparatuses cleaned between trials to eliminate olfactory cues.The released dataset includes raw neuroimaging data (NIfTI format) and raw behavioral video files (AVI format) corresponding to six experimental phases per mouse. No derived behavioral metrics, processed imaging outputs, or statistical summaries are included. File organization and naming are consistent across animals to facilitate reuse. As with most awake imaging datasets, individual differences in motion and signal quality may be present; no manual exclusion of scans or time points has been performed, allowing users to apply their own quality control criteria.This dataset is intended to support studies of awake mouse functional and structural connectivity, individual and sex-related variability, and brain–behavior relationships, as well as methodological development and cross-species neuroimaging research.
description: This dataset was generated as part of the Awake Mouse Connectome Project (AMCP), which aims to establish a large-scale, standardized resource of awake mouse neuroimaging and behavioral data for investigating whole-brain structure, functional connectivity, and their relationships with behavior under physiologically relevant conditions. The present public release includes data from 212 adult C57BL/6N mice, acquired under fully awake conditions, together with synchronized behavioral video recordings.All mice were 8 weeks of age at the start of the experiments and were purchased one week prior to data collection to allow acclimation to the laboratory environment. Animals were group-housed by sex (no more than five per cage) in individually ventilated cages under a 12-hour light/dark cycle, with controlled temperature and humidity and ad libitum access to food and water. All experimental procedures were conducted under standardized conditions to minimize environmental variability.To enable awake MRI acquisition, each mouse underwent surgical implantation of a custom-made, MRI-compatible head holder. Surgeries were performed under isoflurane anesthesia, with body temperature maintained throughout the procedure. After exposing and cleaning the skull, the head holder was secured using dental adhesive and light-cured dental resin to ensure long-term stability. A transparent dental cement layer was applied to protect the exposed skull and facilitate postoperative monitoring. Postoperative analgesia was administered continuously for one week, followed by a recovery period prior to habituation.After recovery, mice underwent a 14-day habituation protocol designed to acclimate them to head fixation and scanner acoustic noise. During habituation, animals were secured in a custom MRI-compatible animal bed and exposed to recorded MRI sounds with gradually increasing intensity and duration. By the final stage, mice were exposed to sound levels and durations equivalent to those used during actual scanning. No rewards were provided during habituation.MRI data were acquired at Changping Laboratory using a 9.4 Tesla small-animal MRI system(uMR, United Imaging Life Science Instrument, Wuhan, China), equipped with an 86-mm volume transmit coil and a four-channel mouse head surface receive coil. For each mouse, high-resolution T2-weighted structural images, resting-state BOLD functional MRI, and diffusion tensor imaging (DTI) data were collected. T2-weighted images covered the whole brain with a spatial resolution of 0.1 × 0.1 × 0.5 mm³. Resting-state functional MRI was acquired using a gradient-echo EPI sequence under awake conditions, consisting of four runs per animal, each yielding 480 usable volumes after initial dummy scans, for a total of 1920 time points per mouse. The temporal resolution was 1 second, with a voxel size of 0.15 × 0.15 × 0.5 mm³. Field maps and pairs of EPI images with opposite phase-encoding directions were acquired to support correction of susceptibility-induced distortions. DTI data were acquired using a multi-shot diffusion-weighted EPI sequence with isotropic 0.2 mm resolution, including one non-diffusion-weighted volume and 32 diffusion-weighted directions at two b-values (800 and 1600 s/mm²). All MRI data are provided as raw NIfTI files without preprocessing.Within one week following MRI acquisition, all mice underwent a battery of freely moving behavioral tests to ensure temporal proximity between imaging and behavioral assessments. The behavioral assays included the open field test, novel object recognition test, and Y-maze tests assessing spontaneous alternation and novel arm preference. The Y-maze protocol consisted of sequential exploration, familiarization, and recall phases, while the open field and object recognition tasks were conducted in a square arena across multiple phases. All behavioral sessions were video recorded under standardized conditions, with apparatuses cleaned between trials to eliminate olfactory cues.The released dataset includes raw neuroimaging data (NIfTI format) and raw behavioral video files (AVI format) corresponding to six experimental phases per mouse. No derived behavioral metrics, processed imaging outputs, or statistical summaries are included. File organization and naming are consistent across animals to facilitate reuse. As with most awake imaging datasets, individual differences in motion and signal quality may be present; no manual exclusion of scans or time points has been performed, allowing users to apply their own quality control criteria.This dataset is intended to support studies of awake mouse functional and structural connectivity, individual and sex-related variability, and brain–behavior relationships, as well as methodological development and cross-species neuroimaging research.