CIAtah¶

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Created by Biafra Ahanonu, PhD.

CIAtah (pronounced cheetah, formerly calciumImagingAnalysis [CIAPKG]) is a software package for analysis of one- and two-photon calcium imaging datasets.

Download the software at https://github.com/bahanonu/calciumImagingAnalysis.

• This user guide contains instructions to setup, run, and troubleshoot CIAtah.
• Note: CIAtah is a class (ciatah within MATLAB) with various GUIs to allow processing of calcium imaging data. In addition, users can access the underlying CIAtah functions to make custom workflows. See Custom command-line pipelines.
• Read my overview of calcium imaging analysis methods at Calcium imaging cell identification and fluorescence activity trace reconstruction, part 1.

Movie processing, cell extraction, and analysis validation.

CIAtah cell sorting GUI

Stable cell alignment across imaging sessions.

CIAtah features:

• Includes a GUI to allow users to do large-scale batch analysis, accessed via the repository's CIAtah class.
• The underlying functions can also be used to create GUI-less, command line-ready analysis pipelines. Functions located in ciapkg and +ciapkg sub-folders.
• Includes all major calcium imaging analysis steps: pre-processing (motion correction, spatiotemporal downsampling, spatial filtering, relative fluorescence calculation, etc.), support for multiple cell-extraction methods, automated cell classification (coming soon!), cross-session cell alignment, and more.
• Has several example one- and two-photon calcium imaging datasets that it will automatically download to help users test out the package.
• Includes code for determining animal position (e.g. in open-field assay).
• Supports Neurodata Without Borders data standard (see calcium imaging tutorial) for reading/writing cell-extraction (e.g. outputs of PCA-ICA, CELLMax, CNMF, CNMF-E, etc.). Supports reading and writing NWB movie files with continued integration with NWB planned.
• Requires MATLAB.

Navigation¶

The main sections of the site:

• Setup - installation of CIAtah.
• Repository - notes about the software package and data formats.
• Processing data - sections related to processing calcium imaging movies using the CIAtah class.
• API - details how to run CIAtah from the command line. Will include more details on the many underlying functions in the future.
• Help - several section that provide hints and help for processing calcium imaging.
• Misc - miscellaneous information about the repository.

References¶

Please cite our Corder, Ahanonu, et al. Science, 2019 publication if you used the software package or code from this repository to advance or help your research.

Questions?¶

Please open an issue on GitHub or email any additional questions not covered in the repository to bahanonu [at] alum.mit.edu.

Made in USA.

• (starting 2020.09.16)
• (starting 2020.09.22)