Compare Neural Circuit Correlations Across States¶

This tool uses 1.0 compute credits per hour.

Overview¶

Compare Neural Circuit Correlations Across States tool calculates pairwise correlations between cell traces within a cell set for each specified state. It uses activity during the states indicated in the annotation file to find these correlations. The tool then compares the differences in correlations during these states.

Input Data¶

To run this tool, IDEAS users must have an .isxd cell set file and a synchronized annotation file.

Valid Inputs¶

Source Parameter	File Type	File Format
Cell Set Files	cell_set	isxd
Annotations File	experiment_annotations	parquet

Generating synchronized annotation files

You can generate the synchronized annotation file by running one of these synchronization tools:

Parameters¶

This tool can accept no state, a single state, or two states. If no state is specified, correlations will be calculated across the entire recording. Otherwise, correlations will be calculated for each state identified and during a non-state period. It is important to note that if there are fewer than 10 frames in the recording during a particular state, correlations will not be calculated for that state. If there are more than 10 frames of data that is not assigned to any state, a "non-state" will be created. If only one state is specified, the effect size will be calculated between that state and the "non-state". If two states are specified, the effect size will be calculated between the two states.

Parameter	Required?	Default	Description
Cell Set Files	True	N/A	ISXD cell set file(s)
Annotations File	False	N/A	File containing annotations about states, synchronised to ISXD cell set file
Column Name	True	state	Column name in annotations file that identifies state
State A	False	N/A	Name of first state
State B	False	N/A	Name of second state
Statistic	True	max	Statistic of correlation to compare (max, mean or min)

Algorithm details¶

graph TD A[Compute correlation matrices] --> B[Plot correlation matrices]; A[Compute correlation matrices] --> C[Find max of correlation matrices]; C[Find max of correlation matrices] --> D[Permutation test of state correlations]; C[Find max of correlation matrices] --> E[Cohen's D of state correlations]; C[Find max of correlation matrices] --> F[Plot cumulative distribution factor]; C[Find max of correlation matrices] --> G[Plot max correlation of cells against each state];

Outputs¶

The tool will generate the following outputs:

File	Format	Description
Maximum correlations data file	CSV	the maximum correlations found in each state, as well as during the non-state period as columns, cells as rows
Raw correlations data file	HDF5	A HDF5 file containing raw correlation matrix for each state

Previews¶

The tool will also generates two previews of the output data:

Correlation Heat Maps¶

This preview will display correlation heat maps for each state specified in the annotation file and a heat map for all data not in any specified state. The data points are reorganized using hierarchical clustering so that groups of highly correlated variables are next to each other. The diagonal entries in the correlation matrices are set to zero.

Effect Size¶

This preview consists of two plots. The first plot shows the cumulative distribution function (CDF) of the correlation for each state specified. The second plot shows a scatterplot of the max correlation during State 1 compared against State 2, and shows the Cohen's d and p-value between the two populations.