https://doi.org/10.5061/dryad.k3j9kd5js

Description of the data and file structure

See methods of associated paper for details on the creation of the dataset

Files include:

*cfos_density_byregionand_timepoint.csv
Associated with figure 4 of the paper. This is the cfos cell density for individual fish for each brain region at each time point.

Data fields

• fish.id: internal reference for the individual fish
• Sex: Sex of the animals (male or female)
• Time point: Which time point the animals were euthanized, either off the housing rack (rack), after remaining in their hometank (Home tank) or time after exposure to the novel tank test (5, 15, 30, 60, or 120 minutes)
• Brain regions: Abbreviations for brain regions; full region names are in Extended table 5-1 of the published manuscript and taken from the adult zebrafish brain atlas (azba.wayne.edu; Kenney et al, 2021) and are available in this repository in "Brain_region_names_and_ontological_levels.csv" 

Extended_table_5-2_15min_vs_HT_cell_counts.csv
Associated with figure 5 of the paper.
This is the average counts per brain region for the home tank and fifteen minute groups, associated p-values from t-tests for each brain region, the effect size (Cohen's D) and the fdr corrected p-value.
Data fields
IDX: Region index number (from azba.wayne.edu; Kenney et al, 2021), can also be found in "Brain_region_names_and_ontological_levels.csv"
Abbreviation: Abbreviation for brain region
Name: Full name of brain region
Home.tank.mean: Average cfos density for each brain region from the hometank fish
fifteen.minute.mean: Average cfos density for each brain region from the group of fish euthanized fifteen minutes after the novel tank test
fold.change: The fold increase in cfos density in the 15 minute group versus the hometank group
p.value: The p-value from the independent samples t-test comparing the hometank to the 15 minute group
cohens.D: The effect size (Cohen's D) for the comparison between the hometank and the 15 minute group
fdr: False discovery rate (FDR) corrected p-values

15min_correlation_matrix.csv
Associated with figure 6 of the paper.
Each row and column represent a brain region (abbreviated). Each entry is the correlated cfos activity between those brain regions across animals for the group of fish euthanized 15 minutes after the novel tank test.

Graph_15min.graphml and Graph_15min.cys
Associated with figure 7 of the paper. The 15 minute correlation with the top 2.5% of correlations to generate a network. In these network files, the nodes represent brain regions and the edges between nodes represent the presence of above threshold correlations. The .cys file is a Cytoscape session file that can be used to look at the network using Cytoscape (https://cytoscape.org/).

Brain_region_names_and_ontological_levels.csv
List of brain regions, abbreviations, index numbers, and ontological levels. These correspond to the adult zebrafish brain atlas (AZBA) nomenclautre (azba.wayne.edu; Kenney et al , 2021).
Data fields
IDX: Region index number
Abbreviation: The abbreviation for the brain region
Name: The full name of the brain region
Ont.1-6: The ontological levels for each region from most coarse/highest (1) to finest (2)
Display: The ontological level used for display in figure 6 of the associated paper.

Bench_protocol_for_whole_brain_activity_mapping.docx
Detailed bench protocol for performing whole-brain activity mapping in adult zebrafish using iDISCO, CellFinder, and ANTs (advanced normalization tools) for registration to the adult zebrafish brain atlas. 

References
Kenney, J.W., Steadman, P.E., Young, O., Shi, M.T., Polanco, M., Dubaishi, S., Covert, K., Mueller, T. and Frankland, P.W., 2021. A 3D adult zebrafish brain atlas (AZBA) for the digital age. Elife, 10, p.e69988.

Code/software

remove_overlaps.py
Python code for removing overlaps after CellFinder:

Kenney_Data_setup_cellfinder_registration.R
R code for combining the output of segmentation from ANTS and cell counts from CellFinder: