-Features:
-- Includes a GUI with different modules to allow users to do large-scale batch analysis, accessed via the repository's `ciatah` class.
+`CIAtah` features:
+- A GUI with different modules to allow users to do large-scale batch analysis, accessed via the repository's `ciatah` class.
- The underlying functions can 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 (CELLMax, PCA-ICA, CNMF, CNMF-E, EXTRACT, etc.), manual classification via GUIs, automated cell classification (coming soon!), cross-session cell alignment, and more.
+- Includes all major calcium imaging analysis steps: movie visualization (including reading from disk), pre-processing (motion correction, spatiotemporal downsampling, spatial filtering, relative fluorescence calculation, etc.), support for multiple cell-extraction methods (CELLMax, PCA-ICA, CNMF, CNMF-E, EXTRACT, etc.), manual classification via GUIs, 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](https://www.nwb.org/) data standard (see [calcium imaging tutorial](https://neurodatawithoutborders.github.io/matnwb/tutorials/html/ophys.html)) 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 planned.
@@ -48,7 +48,7 @@ Made in USA.- CIAtah sell sorting GUI + CIAtah cell sorting GUI
![@@ -106,6 +106,15 @@ obj % then hit enter, no semicolon! - [Optional] Users on Windows systems should download `Everything` (https://www.voidtools.com/). It is a very useful and extremely fast search engine for files and folders on a computer that can allow users to quickly get full paths for lists of folders that need to be analyzed in `CIAtah`. - [Optional] Users who want to analyze data via the command line can run `edit ciapkg.demo.cmdLinePipeline` and run each segment of code there to see what commands are needed to perform each step. It assumes you have already run `example_downloadTestData`. +### Visualize any movie quickly using read from disk + +Users can quickly visualize movies in any of the supported formats (HDF5, AVI, TIFF, and ISXD) using the `playMovie` function. This will read directly from disk, allowing users to scroll through frames to visually check movies before or after processing. See below code: + +```MATLAB +% Use the absolute path to the movie file or a valid relative path. +playMovie('ABSOLUTE\PATH\TO\MOVIE'); +``` + ## Quick start (command line) After downloading `CIAtah` and running the setup as above, users interested in command-line processing can open up the example M-file by running the below command. By running individual code-block cells, users are guided from pre-processing through cell-extraction to cross-session analysis.](https://user-images.githubusercontent.com/5241605/100851700-64dec280-343a-11eb-974c-d6d29faf9eb2.gif){kind=link}