DOI: 10.5061/dryad.zgmsbccng
title: Valence and salience encoding in the central amygdala

description: The central amygdala (CeA) has emerged as an important brain region for
 regulating both negative (fear and anxiety) and positive (reward)
 affective behaviors. The CeA has been proposed to encode affective
 information in the form of valence (whether the stimulus is good or bad)
 or salience (how significant is the stimulus), but the extent to which
 these two types of stimulus representation occur in the CeA is not known.
 Here, we used single cell calcium imaging in mice during appetitive and
 aversive conditioning and found that majority of CeA neurons (~65%) encode
 the valence of the unconditioned stimulus (US) with a smaller subset of
 cells (~15%) encoding the salience of the US. Valence and salience
 encoding of the conditioned stimulus (CS) was also observed, albeit to a
 lesser extent. These findings show that the CeA is a site of convergence
 for encoding oppositely valenced US information.
description: The 1-photon calcium imaging data were pre-processed and
 motion-corrected using the Inscopix Data Processing Software (IDPS). Cell
 identification was performed with a constrained non-negative matrix
 factorization algorithm for microendoscopic data (CNMF-E) within IDPS. All
 cell traces were then statistically tested using the 'circular
 shifting' method to determine whether their responses were
 significant. The code for the circular shifting method is available at
 https://github.com/zweifellab?tab=repositories. ++ Additionally, circular shift analysis tools (R base) have been uploaded in this dataset. 
description: # Valence and Salience Encoding in the Central Amygdala
 [https://doi.org/10.5061/dryad.zgmsbccng](https://doi.org/10.5061/dryad.zgmsbccng) ## Description of the data and file structure All zip files contain data from 1-photon single-cell calcium imaging. Please refer to the variable explanations for detailed information. Behavioral data has also been uploaded. Please see the variable explanations for further details. ### Files and variables #### File: Figure3.zip **Description:**  All data are stored in the file Figure 3.mat. Figure 3C,D: 1.     **HE_perievent**: This variable represents the averaged head entry (HE) activity, spanning from -10 seconds to +10 seconds relative to an event. The data are from PavD1 (1078 cells) and PavD10 (872 cells) sessions, with a sampling rate of 10 Hz (200 data points). 2.     **HE_ResponseIndex**: This variable contains the IDs of neurons categorized based on their responses to head entries. Neurons are classified as excited, inhibited, or not significantly responsive. The data includes responses from both PavD1 and PavD10 sessions. 3.     **HE_AUC**: This variable represents the area under the curve (AUC) during the 0 to 5 second period for neurons classified as excited or inhibited. The data are from PavD1 and PavD10 sessions. Figure 3E-H: 4.     **PavD10_RawData**: Contains raw data from 872 neurons across 20 trials, with 598 datapoints per trial. The data spans from -30 seconds to +29.8 seconds relative to the CS onset. 5.     **PavD10_Zscored_Data**: Z-scores were calculated using the pre-CS period, defined as -10 seconds to 0 seconds before CS onset. 6.     **PavD10_perievent**: This variable represents the averaged neural activity from -30 seconds to +29.8 seconds relative to the event. Datapoint 301 marks CS onset, and datapoint 431 indicates US delivery, which occurred 13 seconds after CS onset. The data was sampled at 10 Hz. 7.     **PavD10_ResponsiveIndex**: This variable includes the IDs of neurons that were classified as excited, inhibited, or not significantly responsive to the CS or US stimuli. #### File: Figure4.zip **Description:**  All data are stored in the file Figure 4.mat. Figure 4A-E: 1.     **Fear_RawData**: Contains raw data from 519 neurons across 10 trials, with 598 datapoints per trial. The data covers the period from -30 seconds to +29.8 seconds relative to CS onset. 2.     **Fear_Zscored_Data**: Z-scores were calculated based on the pre-CS period, defined as -10 seconds to 0 seconds before CS onset. 3.     **Fear_perievent**: Represents averaged neural activity from -30 seconds to +29.8 seconds relative to the event. Datapoint 301 marks CS onset, and datapoint 431 corresponds to US delivery, which occurred 13 seconds after CS onset. The data was sampled at 10 Hz. 4.     **Fear_ResponsiveIndex**: This variable lists the IDs of neurons that were classified as excited, inhibited, or not significantly responsive to the CS or US stimuli. #### File: Figure5.zip **Description:**  All data are stored in the file Figure 5.mat. Salience Cells: 1.     **SalienceCell_Index**: Contains the IDs of neurons classified as salience cells. Neurons labeled as CS_pos_pos showed excitation in response to both food (first "pos") and shock (second "pos"). 2.     **SalienceCell_CS**: Perievent data for CS-responsive salience neurons, spanning from -30 seconds to +29.8 seconds relative to CS onset (t=0 at 301 datapoint, US onset at t=13 or 431 datapoint). Data is sampled at 10 Hz. o   pos_pos1: Food-related activity of CS-excited salience cells. o   pos_pos2: Shock-related activity of CS-excited salience cells. 3.     **SalienceCell_US**: Perievent data for US-responsive salience neurons, with the same time window (-30 s to +29.8 s) and sampling rate as for CS. o   pos_pos1: Food-related activity of US-excited salience cells. o   pos_pos2: Shock-related activity of US-excited salience cells. 4.     **SalienceCell_AUC_US**: Area under the curve (AUC) for US-responsive salience neurons over the 0 to 10-second window. o   pos_pos1: Food-related activity of US salience cells. o   pos_pos2: Shock-related activity of US salience cells. Valence Cells: 5.     **ValenceCell_Index**: Contains the IDs of neurons categorized as valence cells. Neurons labeled as CS_pos_neg were excited by food (first "pos") and inhibited by shock (second "neg"). 6.     **ValenceCell_CS**: Perievent data for CS-responsive valence neurons, spanning from -30 seconds to +29.8 seconds (t=0 at 301 datapoint, US onset at t=13 or 431 datapoint). Data is sampled at 10 Hz. o   pos_neg1: Food-related activity of CS-excited valence cells. o   pos_neg2: Shock-related activity of CS-inhibited valence cells. 7.     **ValenceCell_US**: Perievent data for US-responsive valence neurons, with the same time window (-30 s to +29.8 s) and sampling rate as for CS. o   pos_neg1: Food-related activity of US-excited valence cells. o   pos_neg2: Shock-related activity of US-inhibited valence cells. 8.     **ValenceCell_AUC_US**: Area under the curve (AUC) for US-responsive valence neurons over the 0 to 10-second window. o   pos_neg1: Food-related activity of US valence cells. o   pos_neg2: Shock-related activity of US valence cells. #### File: Figure3\_supplement1.zip **Description:**  All data are stored in the file Figure3_supplement1.mat. Figure 3_figure supplement 1A,B: All data are from **appetitive day 10**. 1. **CS_US_Index**: Contains the IDs of neurons responsive to both CS and US. Neurons labeled as pos_pos were excited by both the CS and the US. 2. **CS_US_perievent**: Perievent data showing averaged neuronal activity from -30 seconds to +29.8 seconds relative to CS onset (t=0 at 301 datapoint, US delivered at t=13 or 431 datapoint). Data is sampled at 10 Hz. Figure 3_figure supplement 1C-F: All data are from **appetitive day 10**. 1. **Early_Late_perievent**: Perievent data showing averaged neuronal activity between early trials (first 5 trials) and late trials (last 5 trials), spanning from -30 seconds to +29.8 seconds relative to CS onset (t=0 at 301 datapoint, US delivered at t=13 or 431 datapoint). Data is sampled at 10 Hz. 2. **Early_Late_AUC**: Area under the curve (AUC) of responsive cells, comparing early trials to late trials, over the 0 to 10-second window. 3. **PavD10_ResponsiveIndex**: Contains the IDs of neurons that were excited, inhibited, or not significantly responsive to the CS/US. #### File: Figure4\_supplement1.zip **Description:**  All data are stored in the file Figure4_supplement1.mat. Figure 4_figure supplement 1A,B: All data are from **aversive day 1**. 1. **CS_US_Index**: Contains the IDs of neurons that are responsive to both CS and US. Neurons labeled as pos_pos were excited by both the CS and the US. 2. **CS_US_perievent**: Averaged neuronal activity from -30 seconds to +29.8 seconds relative to CS onset (t=0 at 301 datapoint, US delivered at t=13 or 431 datapoint). Data is sampled at 10 Hz. Figure 4_figure supplement 1C-F: All data are from **aversive day 1**. 1. **Early_Late_perievent**: Averaged neuronal activity from -30 seconds to +29.8 seconds, comparing early trials (first 5 trials) to late trials (last 5 trials). CS onset is at t=0 (301 datapoint) and US is delivered at t=13 (431 datapoint). Data is sampled at 10 Hz. 2. **Early_Late_AUC**: Area under the curve (AUC) of responsive cells, comparing early trials to late trials over the 0 to 10-second window. 3. **Fear_ResponsiveIndex**: Contains the IDs of neurons that were excited, inhibited, or not significantly responsive to the CS/US. #### File: Figure5\_supplement1.zip **Description:**  All data are stored in the file Figure5_supplement1.mat. Figure 5_figure supplement 1A,B: 1. **PeakZ_Latency_Food**: Contains the peak Z-scores (1st column) and corresponding latencies (2nd column) for food-excited neurons. 2. **PeakZ_Latency_Shock**: Contains the peak Z-scores (1st column) and corresponding latencies (2nd column) for shock-excited neurons. Figure 5_figure supplement 1E-J: All data are from **baseline and posttest**. 1. **Baseline_perievent**: Averaged neuronal activity from -30 seconds to +29.8 seconds. Time (t=0) corresponds to CS onset (301 datapoint). Data is sampled at 10 Hz, including responses to CS1 and CS2. 2. **Posttest_perievent**: Averaged neuronal activity from -30 seconds to +29.8 seconds. Time (t=0) corresponds to CS onset (301 datapoint). Data is sampled at 10 Hz, including responses to CS1 and CS2. #### File: Figure5\_supplement2.zip **Description:**  All data are stored in the file Figure5_supplement2.mat. 1.     **PavD10_ranksum_perievent**: This dataset contains averaged neuronal activity from -30 seconds to +29.8 seconds around the CS onset. Time (t=0) corresponds to CS onset (301 datapoint), with US delivery occurring 13 seconds after CS onset (431 datapoint). The data is sampled at a rate of 10 Hz and was analyzed using a rank-sum test. 2.     **PavD10_ranksum_ResponsiveIndex**: This variable includes the IDs of neurons categorized as excited, inhibited, or not significantly responsive to CS/US. The responses were tested using a rank-sum test. 3.     **Fear_ranksum_perievent**: This dataset contains averaged neuronal activity from -30 seconds to +29.8 seconds around the CS onset. Time (t=0) corresponds to CS onset (301 datapoint), with US delivery occurring 13 seconds after CS onset (431 datapoint). The data is sampled at a rate of 10 Hz and was analyzed using a rank-sum test. 4.     **Fear_ranksum_ResponsiveIndex**: This variable includes the IDs of neurons categorized as excited, inhibited, or not significantly responsive to CS/US. The responses were tested using a rank-sum test. #### File: Figure5\_supplement3.zip **Description:**  All data are stored in the file Figure5_supplement3.mat. **Group 1**: Appetitive → Aversive (165 cells)\ **Group 2**: Aversive → Appetitive (138 cells) 1.     **Salience_Index_Group1**: This variable contains the IDs of salience cells identified in Group 1. 2.     **Salience_Index_Group2**: This variable contains the IDs of salience cells identified in Group 2. 3.     **Valence_Index_Group1**: This variable contains the IDs of valence cells identified in Group 1. 4.     **Valence_Index_Group2**: This variable contains the IDs of valence cells identified in Group 2. 5.     **CS_perievent**: This dataset includes the averaged activity of CS-responsive cells from Groups 1 and 2, measured from -10 seconds to +25 seconds around the CS onset. Time (t=0) corresponds to the CS/US onset (101 datapoint), with a sampling rate of 10 Hz. 6.     **US_perievent**: This dataset includes the averaged activity of US-responsive cells from Groups 1 and 2, measured from -10 seconds to +25 seconds around the US onset. Time (t=0) corresponds to the CS/US onset (101 datapoint), with a sampling rate of 10 Hz. 7.     **CS_AUC**: This variable represents the area under the curve of CS-responsive cells from Groups 1 and 2, calculated from 0 seconds to 10 seconds. 8.     **US_AUC**: This variable represents the area under the curve of US-responsive cells from Groups 1 and 2, calculated from 0 seconds to 10 seconds. #### File: Behavioral\_data..xlsx **Description:**  Figure 1 tap ##### Variables * Time near hopper (seconds) during the appetitive conditioning (10 animals, 10 days)..  * Latency to procure a pellet (seconds) during the appetitive conditioning (10 animals, 10 days)..  * Success rate (%) during the appetitive conditioning (10 animals, 10 days).  * Freezing (%) during the aversive conditioning (10 animals, 10 trials).  Figure5_supplement1 tap ##### Variables * Baseline: Freezing (%) during Food CS and Shock CS (10 animals). * Posttest: Freezing (%) during Food CS and Shock CS (10 animals). ## Code/software Zip files are all MATLAB (.mat) based files.  Circular shifting analysis tools are found in [https://github.com/zweifellab?tab=repositories.](https://github.com/zweifellab?tab=repositories) ++ Additionally, circular shifting analysis tools have been added to this data set.  This code implements the circular shift method to test neuronal responses, using the term 'wrapping' to describe the process, which is synonymous with circular shifting. Example datasets are available at [https://doi.org/10.5061/dryad.zgmsbccng](https://doi.org/10.5061/dryad.zgmsbccng). The file name is 'dataforcircularshift.zip,' and it includes data representing appetitive conditioning on day 10 (d10), aversive conditioning on day 11 (d11), and the post-test phase on day 12 (d12). All datasets must be converted to a format readable by R. Use the 'csv_to_R.R' file to perform the conversion. An example CSV file, 'd10.csv,' has been uploaded within the dataset. *  **Data structure:** 1. **d10**: 872 neurons, 20 trials, 720 data points per trial. Sampling rate is 10 Hz. The CS was delivered at data point 301, and the US at data point 431. 2. **d11**: 519 neurons, 10 trials, 598 data points per trial. Sampling rate is 10 Hz. The CS was delivered at data point 301, and the US at data point 431. 3. **d12**: 788 neurons, 10 trials for CS-food and 10 trials for CS-shock. The two CSs alternate. 598 data points per trial. Sampling rate is 10 Hz. The CS was delivered at data point 301. * **generating_script.R**: This R script generates all the results. - **auxiliary_functions.R**: This R script contains helper functions used by generating_script.R, including functions for plotting neurons and implementing the algorithms outlined in the attached PDF. * **results/**: This folder contains CSV files with p-values, response directions, and other data for both the food/tone tasks. Each CSV file is structured with neurons as rows, and columns contain details such as p-values and response directions.