# ConfUSIus

> Python package for analysis and visualization of functional ultrasound imaging data.

This file describes ConfUSIus version 0.9.0.dev0. ConfUSIus is a Python library built on xarray for loading, registering, extracting signals from, and visualizing functional ultrasound imaging (fUSI) data. Every spatial array is a VoxelData `xarray.DataArray` with dims `(..., time, pose, k, j, i)` and a voxel-to-world affine index. Install with `pip install confusius`. The package is in beta and the API may change between releases.

## User guide

- [Getting Started](<https://confusius.tools/dev/user-guide/getting-started/index.md>)
- [Installation](<https://confusius.tools/dev/user-guide/installation/index.md>)
- [Input/Output](<https://confusius.tools/dev/user-guide/io/index.md>)
- [The VoxelData Model](<https://confusius.tools/dev/user-guide/voxeldata/index.md>)
- [Working with Xarray](<https://confusius.tools/dev/user-guide/xarray/index.md>)
- [Multi-Pose Imaging](<https://confusius.tools/dev/user-guide/multipose/index.md>)
- [Beamformed IQ](<https://confusius.tools/dev/user-guide/beamformed-iq/index.md>)
- [Visualization](<https://confusius.tools/dev/user-guide/visualization/index.md>)
- [Quality Control](<https://confusius.tools/dev/user-guide/quality-control/index.md>)
- [Atlases](<https://confusius.tools/dev/user-guide/atlas/index.md>)
- [Datasets](<https://confusius.tools/dev/user-guide/datasets/index.md>)
- [Registration](<https://confusius.tools/dev/user-guide/registration/index.md>)
- [Temporal Resampling](<https://confusius.tools/dev/user-guide/timing/index.md>)
- [Spatial Processing](<https://confusius.tools/dev/user-guide/spatial/index.md>)
- [Signal Processing](<https://confusius.tools/dev/user-guide/signal/index.md>)
- [Decomposition](<https://confusius.tools/dev/user-guide/decomposition/index.md>)
- [Decoding](<https://confusius.tools/dev/user-guide/decoding/index.md>)
- [Functional Connectivity](<https://confusius.tools/dev/user-guide/connectivity/index.md>)
- [General Linear Model](<https://confusius.tools/dev/user-guide/glm/index.md>)
- [Statistical Inference](<https://confusius.tools/dev/user-guide/stats/index.md>)

## Graphical interface

- [Overview](<https://confusius.tools/dev/gui/overview/index.md>)
- [Using the Plugin](<https://confusius.tools/dev/gui/plugin/index.md>)

## API reference

- [Atlases](<https://confusius.tools/dev/api/atlas/index.md>)
- [fUSI-BIDS](<https://confusius.tools/dev/api/bids/index.md>)
- [Functional Connectivity](<https://confusius.tools/dev/api/connectivity/index.md>)
- [Datasets](<https://confusius.tools/dev/api/datasets/index.md>)
- [Decoding](<https://confusius.tools/dev/api/decoding/index.md>)
- [Decomposition](<https://confusius.tools/dev/api/decomposition/index.md>)
- [Signal Extraction](<https://confusius.tools/dev/api/extract/index.md>)
- [General Linear Model](<https://confusius.tools/dev/api/glm/index.md>)
- [Overview](<https://confusius.tools/dev/api/index.md>)
- [Input/Output](<https://confusius.tools/dev/api/io/index.md>)
- [Beamformed IQ](<https://confusius.tools/dev/api/iq/index.md>)
- [Multi-Pose Imaging](<https://confusius.tools/dev/api/multipose/index.md>)
- [Plotting](<https://confusius.tools/dev/api/plotting/index.md>)
- [Quality Control](<https://confusius.tools/dev/api/qc/index.md>)
- [Registration](<https://confusius.tools/dev/api/registration/index.md>)
- [Signal Processing](<https://confusius.tools/dev/api/signal/index.md>)
- [Spatial Processing](<https://confusius.tools/dev/api/spatial/index.md>)
- [Statistical Inference](<https://confusius.tools/dev/api/stats/index.md>)
- [Temporal Resampling](<https://confusius.tools/dev/api/timing/index.md>)
- [Data Validation](<https://confusius.tools/dev/api/validation/index.md>)
- [Xarray Integration](<https://confusius.tools/dev/api/xarray/index.md>)

## Examples

- [Atlas-based region correlation matrix](<https://confusius.tools/dev/examples/_built/connectivity/atlas_correlation_matrix/index.md>)
- [Atlas-based seed connectivity maps](<https://confusius.tools/dev/examples/_built/connectivity/atlas_seed_map/index.md>)
- [Searchlight decoding of a continuous variable](<https://confusius.tools/dev/examples/_built/decoding/searchlight_speed/index.md>)
- [FastICA on a single fUSI recording](<https://confusius.tools/dev/examples/_built/decomposition/fastica_single_recording/index.md>)
- [NMF on a single fUSI recording](<https://confusius.tools/dev/examples/_built/decomposition/nmf_single_recording/index.md>)
- [PCA on a single fUSI recording](<https://confusius.tools/dev/examples/_built/decomposition/pca_single_recording/index.md>)
- [First-level GLM analysis of fUSI data](<https://confusius.tools/dev/examples/_built/glm/first_level/index.md>)
- [Lagged first-level GLM analysis of fUSI data with a continuous regressor](<https://confusius.tools/dev/examples/_built/glm/first_level_continuous/index.md>)
- [ConfUSIus and Xarray 101](<https://confusius.tools/dev/examples/_built/io/confusius_xarray_101/index.md>)
- [Create a VoxelData array from a MAT file](<https://confusius.tools/dev/examples/_built/io/create_voxeldata_from_mat/index.md>)
- [The ConfUSIus Dataset Collection](<https://confusius.tools/dev/examples/_built/io/dataset_collection/index.md>)
- [Load multi-pose recordings](<https://confusius.tools/dev/examples/_built/io/load_multipose_recordings/index.md>)
- [Register a recording to an Allen fUSI template](<https://confusius.tools/dev/examples/_built/registration/register_to_allen_fusi_template/index.md>)
- [Registration of two sessions from the same subject](<https://confusius.tools/dev/examples/_built/registration/register_volume_same_subject/index.md>)
- [Motion correction of a single recording](<https://confusius.tools/dev/examples/_built/registration/volumewise_motion_correction/index.md>)

## Optional

- [Changelog](<https://confusius.tools/dev/changelog/index.md>)
- [Community](<https://confusius.tools/dev/contributing/index.md>)
- [Citing](<https://confusius.tools/dev/citing/index.md>)