Command-line processing, GUI/features updates playMovie, signalSorter, increased NWB support, and more.

Changelog
Version: v3.20.20201019131033.

This release contains large usability updates to signalSorter and playMovie to make GUIs more responsive and user friendly. Also updated command-line examples and processing for users along with adding additional helper functions and other updates.

New

• ciapkg.demo.runPreprocessing - Addition to allow users to run pre-processing on a movie from a single function. To be expanded later.
• ciapkg.io.getMovieInfo - Wrapper to quickly get movie information. Options are the same as loadMovieList.
• ciapkg.io.readFrame - Fast reading of frame from files on disk. This is an alternative to loadMovieList that is much faster when only a single frame needs to be read.
• ciapkg.signal_extraction.runPcaIca - Wrapper to run PCA-ICA (Mukamel, 2009) cell extraction using two existing versions on CIAPKG.

Upated

• playMovie - major update to improve GUI. Updated slider and pause movie callbacks to reduce probability that slider starts to move erratically, move focus away from slider after use (so keyboard callbacks work), and improve pause handling. Made angle optional for options.primaryTrackingPoint. Refactored code to make easier to manage. Middle and right-click of mouse now lead to pausing. Check for NWB input file and change dataset name to accomodate. Create a shortcut menu for easier navigation. Add support for displaying in RGB when reading from AVI movies. Switch read from disk support to using ciapkg.io.readFrame so that playMovie uses the new standard interface for fast reading from disk.
• signalSorter - Display context menu for keyboard shortcuts, easier than separate figure. User can select with right-click or via a menu in the GUI. Users can now scroll through cells using mouse scroll wheel.
• ciapkg.demo.cmdLinePipeline - Updated to add support for cross-session analysis and use ciapkg.demo.runPreprocessing() to process the other imaging sessions. Update to use ciapkg.signal_extraction.runPcaIca for PCA-ICA to make easier for users to run in the future.
• getOptions - Added passArgs option, this mimics the ... construct in R, so users can pass along arguments without having to define them in the calling function (e.g. in the case of wrapper functions).
• applyImagesToMovie - Supports inputMovie as a character path to the movie.
• loadMovieList - Improved comments and options descriptions.
• ciapkg.io.getMovieFileType - addition of a second movie type, e.g. to differentiate NWB even though it is HDF5.
• suptitle - Added support for latex intepreter to allow more detailed information display.
• computeSaleaeOutput - Updated to make more easily usable with other miniscope sync signals. Remove eval call.
• runICA - added IcaOutputInfo output.
• runPCA - Compatibility fixes for matrix inputs.
• changeFont - Added support for changing font type.

Additional

• playMovie - Add support for read from disk for major filetypes, e.g. hdf5, tiff, avi, and isxd. User just needs to input filename. Added frameList to support only looping over specific sequences in the movie.
• example_downloadTestData - added two-photon example data.
• ciapkgRoot - added for future functions to quickly locate the root as needed.
• ciapkg.getDir - allow users to get the directory of ciapkg quickly.
• ciapkg.io.loadIDPS - added to allow central place to load Inscopix IDP ISX package.
• ciapkg.demo.cmdLinePipeline - Use ciapkg.getDir() to make sure demo always calls correct path regardless of where user is pointing. Also make playMovie calls have titles to make clearer to new users and allow a GUI-less option.
• loadMovieList - Change warning message output for HDF5 file of certain type. Add option to suppress warnings.
• turboregMovie - Remove references to parfor_progress.
• computeCnmfSignalExtractionClass - allow option to skip CNN, problematic for certain datasets and not necessary if doing manual classification.
• Added updated NWB support for saving out movies during processing step.
• Misc other changes.

Improved README, GUI, and pre-processing.

Below is a partial list of updates, see individual pull requests for more.

• modelPreprocessMovieFunction now displays options as meaningful names and the strings appended to the filename to indicate processing steps have been made shorter to avoid long filenames.
• loadBatchFxns - Updates to remove additional specific repositories that should not be loaded by default. Add support for overriding this feature.
• Updates to README, logo and link to File Exchange.
• java.opts no longer in root path since MATLAB recommends against using it to change Java Heap Memory in current MATLAB versions. Instead use preferences and see https://www.mathworks.com/help/matlab/matlab_external/java-heap-memory-preferences.html. For older MATLAB versions, move java.opts back to root path.
• runPipeline - Added a check to make sure certain directories are unloaded after running a module if they are not needed.
• ciapkg.loadAllDirs - this ciapkg function will force all directories to load in cases where that is needed.
• signalSorter - Added support for direct loading of NWB files.
• Use example via edit ciapkg.demo.cmdLinePipeline.
• ciapkg.version - moved version checking to a function to allow more flexibility going forward.
• ciapkg.io.dependencyCheck - new function to allow checking of both whether a toolbox has a license and is installed, for cases in which license exists but user has not installed the toolbox.
• loadDependencies, downloadCnmfGithubRepositories, and downloadGithubRepositories - updated to allow forced updating of GitHub repositories even if already downloaded.
• ciapkg.download.updatePathCleanup - clean up functions, Java, etc. in memory to allow updating of GitHub repo dependencies.
• playMovie - support for sparse movies.
• Improved USA flag display :D
• modelPreprocessMovieFunction - Further upgraded adding json to HDF5 directly for later reading out to get settings.
• modelSaveMatchObjBtwnTrials - Allow users to export output from computeMatchObjBtwnTrials.
• getOptions - Support case where calling getOptions from command line or where there is no stack.
• loadMovieList - added support for taking specific channel from RGB AVI.
• The full docs have been added under /docs folder.
• Misc other updates.

Release for File Exchange

• Updated GUI, NWB support, and other changes. See pull requests for details.

Initial release of calciumImagingAnalysis package.

This is the initial release of the calciumImagingAnalysis package comprising code to allow calcium imaging preprocessing, cell extraction, manual cell sorting, and cross-session alignment along with several other functions related to neuro/behavioral analysis (e.g. animal location tracking).

The internal version number is v3.20181211 and will be updated to match the repository versioning in the future. Older versions of the code have been used in previously published studies, see Parker, Nature, 2018.

See README for details on using functions within the package.