CIAtah

<!-- # `CIAtah` (calciumImagingAnalysis [ciapkg]) -->

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CIAtah (pronounced cheetah; formerly <ins>c</ins>alcium<ins>I</ins>maging<ins>A</ins>nalysis [ciapkg]) is a software package for analyzing one- and two-photon calcium imaging datasets. It can also be used to process other imaging datasets (e.g. from non-calcium indicators and dyes).

<img src="https://user-images.githubusercontent.com/5241605/99499485-d6dce500-292d-11eb-8c68-b089fe1985c8.png" width="42%" align="right" alt="ciatah_logo">

CIAtah currently requires MATLAB and runs on all major operating systems (Windows, Linux [e.g. Ubuntu], and macOS).

• Note: CIAtah version v4 moves the remaining (i.e. all except external packages and software) CIAtah functions into the ciapkg package to improve namespace handling and requires MATLAB R2019b or above (due to package import changes).

Full documentation at https://bahanonu.github.io/ciatah/.

Below are recordings and additional documents for users who want to learn more about calcium imaging analysis/experiments and the CIAtah pipeline.

<ins> Book chapter </ins> — We have a book chapter that goes over all steps of miniscope imaging: viral injections, GRIN lens probe implant, pain experimental design, data processing and neural/behavioral analysis, and more.

• See Ahanonu, B., Corder, G. (2022). Recording Pain-Related Brain Activity in Behaving Animals Using Calcium Imaging and Miniature Microscopes (https://doi.org/10.1007/978-1-0716-2039-7_13).

<ins>Webinar</ins> — This webinar gives an overview of calcium imaging analysis (with a focus on CIAtah) along with tips for improving experiments and analysis: https://info.inscopix.com/inscopix-inspire-view-webinarbiafra-ahanonu-signal-in-the-noise-distinguishing-relevant-neural-activity-in-calcium-imaging.

<ins>Workshop tutorial</ins> — This recording gives an overview of setting up and using CIAtah: https://www.youtube.com/watch?v=I6abW3uuJJw.

<ins>Imaging analysis tools</ins> My table with many current imaging analysis tools: https://github.com/bahanonu/imaging_tools.

<ins>GRINjector</ins> — A surgical device to help with implanting gradient-refractive index (GRIN) lens probes into the brain or other regions: https://github.com/bahanonu/GRINjector.

Spinal cord imaging

<ins>New motion correction methods</ins> — Methods for motion correction of spinal imaging data using feature identification (e.g. with DeepLabCut), control point registration, and other methods. Additional updates on integration into CIAtah in the future.

• Publication: B. Ahanonu*, A. Crowther*, A. Kania, M. Rosa-Casillas, A.I. Basbaum. (2024). Long-term optical imaging of the spinal cord in awake behaving mice. Nature Methods. https://doi.org/10.1038/s41592-024-02476-3 (https://www.nature.com/articles/s41592-024-02476-3)
  • Preprint: Ahanonu and Crowther, et al. (2023). Long-term optical imaging of the spinal cord in awake, behaving animals. bioRxiv (https://www.biorxiv.org/content/10.1101/2023.05.22.541477v1.full).
• Documentation for spinal cord motion correction can be found at https://bahanonu.github.io/ciatah/pipeline_detailed_spinal.
• Other documentation for spinal cord imaging at https://github.com/basbaumlab/spinal_cord_imaging.

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Contents

• CIAtah features
• CIAtah example features
• Quick start guide
• Quick start (command-line)
• CIAtah main GUI notes
• Acknowledgments
• References
• Questions
• License

Contact: Biafra Ahanonu, PhD (github [at] bahanonu [dot] com).

Made in USA.<br> <img src="https://user-images.githubusercontent.com/5241605/71493809-322a5400-27ff-11ea-9b2d-52ff20b5f332.png" align="center" title="USA" alt="USA" width="auto" height="50">

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CIAtah features

• CIAtah package-enclosed functions (in +ciapkg sub-folders) can be used to create GUI-less, command line-ready analysis pipelines. As all functions are within the ciapkg package for improve namespace handling to allow incorporating into other programs.
• A GUI, via ciatah class, with different modules for large-scale batch analysis.
• Includes all major calcium imaging analysis steps:
  • movie visualization (including reading from disk, for fast viewing of large movies);
  • pre-processing (motion correction [e.g. TurboReg, NoRMCorre] , spatiotemporal downsampling, spatial filtering, relative fluorescence calculation, etc.);
  <!-- - Pre-processing supports read-from-disk based analysis for movies that are too large to fit into RAM. -->
  • support for multiple cell-extraction methods:
    • <a href='https://github.com/mukamel-lab/CellSort'>PCA-ICA</a>
    • <a href='https://searchworks.stanford.edu/view/11513617'>CELLMax</a> (<a href='https://searchworks.stanford.edu/view/12854822'>additional</a>)
    • <a href='https://github.com/flatironinstitute/CaImAn-MATLAB' target='_blank'>CNMF</a>
    • <a href='https://github.com/zhoupc/CNMF_E'>CNMF-E</a>
    • <a href='https://github.com/schnitzer-lab/EXTRACT-public' target='_blank'>EXTRACT</a>
    • etc.
  • manual classification of cells via GUIs;
  • automated cell classification (i.e. CLEAN algorithm, coming soon!);
  • cross-session cell alignment;
  • and more.
• Includes example one- and two-photon calcium imaging datasets for testing CIAtah.
• Supports a plethora of major imaging movie file formats: HDF5, NWB, AVI, MP4, ISXD [Inscopix], TIFF, BigTIFF, SLD [SlideBook], and Bio-Formats compatible formats (Olympus [OIR] and Zeiss [CZI and LSM] currently, additional support to be added or upon request).
• Supports Neurodata Without Borders data standard (see calcium imaging tutorial) for reading/writing cell-extraction and imaging movie files.
• Animal position tracking (e.g. in open-field assay) via ImageJ plugin.
• Requires MATLAB and runs on all major operating systems (Windows, Linux [e.g. Ubuntu], and macOS).

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CIAtah example features

<p align="center"> <strong>Support for entire calcium imaging pipeline.</strong> </p> <!--  --> <!--  --> <p align="center"> <a href="https://github.com/bahanonu/ciatah/assets/5241605/9236ec16-38a9-40da-8545-ad40d0ea83c3"> <img src="https://github.com/bahanonu/ciatah/assets/5241605/9236ec16-38a9-40da-8545-ad40d0ea83c3" align="center" title="ciapkgMovie" alt="ciapkgMovie" width="100%" style="margin-left:auto;margin-right:auto;display:block;margin-bottom: 1%;"> </a> </p> <p align="center"> <strong>Movie processing, cell extraction, and analysis validation.</strong> </p> <p align="center"> • Press play if auto-play disabled. </p> <p align="center"> <a href="https://user-images.githubusercontent.com/5241605/94530890-9c3db280-01f0-11eb-99f0-e977f5edb304.gif"> <img src="https://user-images.githubusercontent.com/5241605/94530890-9c3db280-01f0-11eb-99f0-e977f5edb304.gif" align="center" title="ciapkgMovie" alt="ciapkgMovie" width="60%" style="margin-left:auto;margin-right:auto;display:block;margin-bottom: 1%;"> </a> </p> <p align="center"> <strong>Cell sorting GUI.</strong> </p> <p align="center"> • Press play if a