About CaliAli

CaliAli is a comprehensive suite designed for extracting neural signals from one-photon calcium imaging data collected across multiple sessions in free-moving conditions. CaliAli incorporates all the necessary modules to extract long-term tracked calcium signals from raw video sessions.

CaliAli Pipeline

Key Features

CaliAli includes the following functions:

Downsampling Videos: Provides functions for downsampling videos.
Motion Correction: Corrects rigid and non-rigid motion artifacts within the field of view.
Automatic Detrending and Preprocessing: CaliAli automatically preprocesses sessions to prepare them for concatenation in subsequent steps.
Alignment of Sessions: Aligns multiple calcium imaging sessions using blood vessel projections obtained from motion-corrected calcium imaging videos.
Neural Signal Extraction: Offers a graphical user interface (GUI) to estimate optimal neural extraction parameters and customize the CNMF-E pipeline for extracting calcium signals from long, concatenated video sequences.
Post-processing and Evaluation: Provides a GUI for easy labeling and identification of false positives.
Manual Extraction of Missed Neurons: Offers a GUI for examining residual images and allowing users to choose new seed pixels to re-execute the extraction process.
Several other functions that facilitate video monitoring and calcium signal tracking throughout the extraction process.

Version History

CaliAli 1.1 Release Notes

April 22nd 2024

Introduced a new app for determining optimal blood vessel (BV) size.
Removed unnecessary or deprecated functions.
Several improvements to the documentation.

Full Changelog on GitHub.

CaliAli Stable Version 1.0 Release Notes

April 19th 2024

We are excited to announce the first stable version of CaliAli, featuring significant enhancements and improvements. Below are the key changes in this release:

Changes:

Full Online Documentation: Access comprehensive documentation to guide you through using CaliAli efficiently.
Optimized Computational Performance: CaliAli is now optimized for low memory requirements, ensuring smoother and more efficient processing.
Improved Session Analysis: Analyze individual sessions and perform multisession concatenation seamlessly.
Enhanced Blood Vessel (BV) Extraction: Minimized vignetting artifacts for improved accuracy in BV extraction.
New BV Stability Metric: Evaluate tracking performance with a new stability metric integrated into BV extraction.
Bug Fixes in GUIs: Addressed several bugs in the graphical user interfaces (GUIs) for improved usability.
Enhanced Inter-Session Alignment: Further improvements to the inter-session alignment module for precise video session alignment.

Full Changelog on GitHub.

CaliAli Beta Release 1.0-beta

May 19th 2023

The first beta release of CaliAli is now available, offering advanced capabilities for extracting neural signals from one-photon calcium imaging data in free-moving conditions.

For details, refer to the BioRxiv preprint.

Explore CaliAli to analyze calcium imaging data with accuracy and efficiency, shaping the future of neural signal extraction in neuroscience research.

GNU General Public License v3.0

CaliAli License

CaliAli-PV/CaliAli is licensed under the GNU General Public License v3.0.

Permissions of this strong copyleft license are conditioned on making available complete source code of licensed works and modifications, which include larger works using a licensed work, under the same license. Copyright and license notices must be preserved. Contributors provide an express grant of patent rights

Permissions (1)
1. - Commercial use
  - Modification
  - Distribution
  - Patent use
  - Private use
Limitations (1)
1. - Liability
  - Warranty
Conditions (1)
1. - License and copyright notice: Must be preserved
  - State changes: Must disclose changes made
  - Disclose source: Source code must be made available
  - Same license: Modifications must be licensed under the same terms

Questions about CaliAli?

We're currently developing a comprehensive Frequently Asked Questions (FAQ) section for CaliAli, coming soon! In the meantime, please don't hesitate to reach out on our discussion board if you have any questions or need assistance.