Dataset DOI: 10.5061/dryad.2rbnzs81t

Description of the data and file structure

All preprocessed data and code (without raw data) can be found in this file: Visual_objects_refine_head_direction_coding.tar

Raw data can be found in this file: Visual_objects_refine_head_direction_coding_rawData.tar

Data files are stored in MATLAB (.mat) or comma-separated value (.csv) format and scripts as MATLAB scripts (.m) or Jupyter notebooks (.ipynb).

Files and variables

Scripts are named after the Figure panel(s) they produce. Data required to produce the figures are stored in the folder “preprocessed data”, and scripts required to for panel production are stored in the folder “codes”.

Data and scripts are stored in subfolders depending on the technique they are associated with ("fUS" (Figure 1) or electrophysiology ("ephys", Figure 2-5)). "epyhs" is further separated in either acutely inserted electrodes ("acute", Figure 2) or chronically implanted electrodes ("chronic", Figures 3-5). Only for Data, "chronic" is further subdivided by experimental design in either data coming from sessions with an arena with a single cue and subsequent head-fixation ("one cue and head-fixed", Figure 3-5) or sessions with two cues present in the arena ("two cues", Figure 5).

Raw data can be found in the folder “raw data” of the file Visual_objects_refine_head_direction_coding_rawData.tar and is stored in different subfolders depending on whether the data was collected in anesthetized (“anes”) or awake (“awake”) mice. These subfolders are further subdivided based on animal identity and recording day. In each folder of a recording day, one raw fUS dataset (.mat, variable “I”) can be found with the corresponding PsychoPy output file (.csv) containing the stimulus information. In the subfolder “fus”, the text file “stimulus and setup information.txt” describes general details of the stimulus timing and setup configuration.

Description of scripts:

Fig1bef_S1b_S2cd.m: In this script, the region-segmented fUS data is loaded, and temporal dynamics of specific or all regions are visualized. This script also produces “TableS1_pValues_segmented_anes.xls” and “TableS1_pValues_segmented_awake.xls” stored in “figures/final panels/Tables” that contain the p-values associated with the panels Fig. 1e,g and Fig. S2c,e.

Fig1c_S1d_S2a.m: This script loads the voxel-wise GLM results of the fUS data and overlays them on the Allen brain atlas.

Fig1d.m: This script visualizes the Object-Preference indices of the fUS data at the voxel-level.

Fig1gh_S4ab_S2ef.m: In this script, the region-segmented fUS data is further analyzed in respect to literature-defined brain networks.

FigS1a.m: This script plots all stimuli used in the fUS experiments.

FigS1c_2b.m: This script plots the region-segmented GLM results of the fUS data on top of the Allen Brain Atlas.

FigS3abc.m: In this script the region-segmented fUS data is further analyzed by different clustering approaches.

FigS3de.m: In this script, the voxel-wise fUS data is further analyzed by k-means clustering.

FigS13.m: This script plots the pupil responses recorded during awake fUS experiments in response to object and control images.

Fig2cdefgh.m: This script analyzes the electrophysiological recordings performed in five different regions of anesthetized mice in response to object and control stimuli.

FigS6.m: This script visualizes all objects and control stimuli used in awake and anesthetized electrophysiological recordings.

FigS7a.m, FigS7b.m and FigS7cd.m: These three scripts describe the analysis for the electrophysiological recordings performed in five different regions of anesthetized mice in response to stimuli aiming to map receptive field size (S7a), temporal frequency tuning (S7b), and spatial frequency tuning (S7cd).

FigS9bcdefg.m: In this script, differences between electrophysiological recording in Postsubiculum from awake and anesthetized mice are analyzed.

FigS9hi.m: This script analyzes the object sensitivity for the ON and OFF responses observed in electrophysiological recordings of the Postsubiculum of anesthetized mice.

Fig3abcdefghij.m: In this script, the analysis of the electrophysiological data recorded in the Postsubiculum of awake mice is provided. Here, the mice were first allowed to freely explore an arena with one landmark, and subsequently, the mice were head-fixed and object and control images were presented to them.

Fig4abcdef_FigS10abcdefghij.m: This script provides further analysis of the above-described data with emphasis on the head-direction cells and their relationship between head-direction coding and visual stimulus responses.

Fig5abcd_S12.m: In this script, the freely-moving epoch of the above-described dataset is further analyzed with emphasis on how the visual landmark influences head-direction coding.

Fig5efg.m: This script provides the analysis of electrophysiological data recorded in the Postsubiculum of awake mice. In this case, the mice were allowed to freely move in an arena containing two landmarks (an image of an object and an image of a scrambled version of this object).

Description of Figures:

Figure 1 (and associated Supplemental Figures S1-S4 and S13): Images of objects and scrambled control stimuli were shown to anesthetized or awake mice while whole-brain blood volume changes were recorded using functional ultrasound imaging.

Figure 2 (and associated Supplemental Figures S5-S7 and S9): Acute electrophysiological recordings in five brain regions were performed in anesthetized mice while showing images of objects and two different types of scrambled control stimuli.

Figures 3-4 (and associated Supplemental Figures S8 and S10-S11): Chronic electrophysiological recordings in Postsubiculum of awake mice; First, the mice were allowed to freely move around in an arena with a single landmark and secondly, the mice were head-fixed, and the same stimuli as in Figure 2 were shown to the mice (images of objects and control stimuli). Panels Figure 4H-L are based on an in silico model described in the script “Fig4hijkl_FigS11.ipynb”.

Figure 5 (and associated Supplemental Figure S12): Further analysis of chronic electrophysiological recordings in Postsubiculum of awake mice. In Figure 5A-D (script “Fig5abcd_S12.m”), the same epoch as described above, where the mice freely moved around in an arena with a single landmark, was analyzed. In Figure 5E-G (script “Fig5efg.m” the mice were placed in an arena with two landmarks (an object and a scrambled version of the same object).

For this Dryad upload, three images of human faces were removed (“PC4_1”, PC4_2”, PC4_3”) from “ephys/all object stimuli” and “fUS/stimuli/PCs”. The original files were obtained from https://fei.edu.br/~cet/facedatabase.html.

Code/software

Matlab and the following toolboxes are required: Curve Fitting Toolbox, Image Processing Toolbox, Statistics and Machine Learning Toolbox, Wavelet Toolbox, Bioinformatics Toolbox, Signal Processing Toolbox