Data accompanying the publication “Midbrain encodes sound detection behavior without auditory cortex” by Lee T-Y, Weissenberger Y, King AJ, Dahmen JC (2024).

Lee_et_al_2024_dataClustering

Folder ‘clustering’ contains the file population_activity.npy which provides the concatenated mean activity of hit and miss trials for each neuron and has been formatted specifically for clustering analysis (https://github.com/leetaiying/lee-et-al-2024).

• Each row contains the activity from one neuron. For each neuron, the mean activity was obtained by taking the mean across all the stimulus trials in a given session separately for hit and miss trials.

• The shape of this dataset is neuron x time point (i.e. imaging frames for hit and miss trials).

  • There are 193 imaging frames per trial in our experiments, so the number of time points for hit and miss trials concatenated are 386 frames.
  • There are 2649 neurons in this dataset in total, the first 1697 neurons were from non-lesioned, and the following 952 neurons were from lesioned mice.

Lee_et_al_2024_data\Behav_2P

Folder ‘Behav_2P’ contains behavioral data and corresponding fluorescence traces of individual neurons obtained with two-photon calcium imaging. Each subfolder contains data from one mouse. The names of those subfolders indicate the mouse ID. Some mice had bilateral auditory cortex lesions.

• IDs of non-lesioned mice: 08, 13, 16, 27, 28, 29, 30, 31, 32
• IDs of mice with (near-)complete lesions: 01, 02, 33, 36
• IDs of mice with partial lesions: 04, 34, 37

Lee_et_al_2024_data\Behav_2P\*mouse-ID*\Day*

• Each mouse ID folder contains subfolders for different days.

• Each day folder contains a file of the recorded fluorescence traces (F.mat) and a file of the corresponding neuropil fluorescence traces (Fneu.mat) for the ROIs obtained on that day.

Lee_et_al_2024_data\Behav_2P\*mouse-ID*\Day*\behaviour

Each day folder also contains a subfolder ‘behaviour’ which contains .txt file recordings of the behaviour from that day.

• Each line of the text file specifies the nature and timing of a behavioural event. The timing of events is specified with respect to the frame number of the two-photon micrcoscope as well as the time that has passed since the behaviour recording was started. The last number of a line indicates the microscope frame number in which the event occurred and the preceding number indicates the time that has passed in seconds since the behaviour recording was started. Fluorescence data were typically recorded in blocks of 13500 or 27000 frames. Fluorescence recordings always started after and finished before the behaviour recording for the given block. Consequently, several events at the end of a behaviour .txt file may indicate the same frame number of 13500 or 27000 indicating that these events occurred after the microscope had stopped recording. F.mat and Fneu.mat provide the concatenated fluorescence data of all recording blocks.

• Event types:

  • ‘Sound:click’: Presentation of a click sound.
    The number after ‘Sound:click’ indicates the attenuation factor [intensity here equals 80dB SPL minus (3dB SPL times attenuation factor)] applied to that click sound.
    • Example 1: ‘Sound:click_7_7.8265_0’ tells us that a click was presented with an attenuation factor of 7 [i.e. an intensity of 59dB SPL (80-(3*7))] at 7.8265 seconds after the behaviour recording started and at microscope frame 0 (i.e. before the microscope started recording).
    • Example 2: ‘Sound:click_0_30.6169_493’ tells us that a click was presented with an attenuation factor of 0 [i.e. an intensity of 80dB SPL (80-(3*0))] at 30.6169 seconds after the behaviour recording started and at microscope frame 493.
  • ‘Sound:catch_trial_99’: Catch trial (i.e. a trial without sound presentation)
    • Example: ‘Sound:catch_trial_99_47.3439_957’ tells us that a catch trial occurred 47.3439 seconds after the bevhaviour recording started and at microscope frame 957.
  • ‘lick:L’: Mouse licked the spout.
    • Example: ‘lick:L_17.4209_128’ tells us that the mouse licked the spout 17.4209 seconds after the behaviour recording started and at microscope frame 128.
  • ‘rew:RL’: Drop of water delivered as reward.
    • Example: ‘rew:RL_17.4263_128’ tells us that a water reward was delivered 17.4263 seconds after the behaviour recording started and at microscope frame 128.

Lee_et_al_2024_data\Behav_2P\Opto

Folder ‘Opto’ contains .mat tables of the behavioural data from three mice performing a sound detection task with and without bilateral optogenetic manipulation of the auditory cortex.

• Column ‘type’ indicates the trial type:
  • ‘click’ = stimulus trial (i.e. a click sound was presented)
  • ‘catch’ = catch trial (i.e. no stimulus was presented)
• Column ‘opto’ indicates whether LEDs for optogenetic stimulation were switched on:
  • ‘mask’ = only the mask LEDs were on.
  • ‘opto’ = both the mask LEDs and optogenetics LEDs were on.
• Column ‘hit’ indicates whether a lick had occurred during the response window:
  • ‘1’ = lick occurred.
  • ‘0’ = no lick occurred.
• Column ‘rt’ indicates response latency in ms.