Updated to license, move functions into ciapkg package, gramm graphics, detrend support, speed improvements, movie controls to CIAtah main GUI, etc.

[bahanonu]

Main features and changes:

• Add sliders to allow users to quickly scroll through both movies in main ciatah GUI.
• Added detrend support for ciatah class modelPreprocessMovieFunction.
• Moved ciapkg overloaded functions into sub-package ciapkg.overloaded to clean up namespace and not interfere with users namespace, updated dependent functions accordingly.
• Moved startup into ciapkg to prevent changing user settings at startup.
• Moved loadBatchFxns into ciapkg package and updated all functions accordingly.
• Speed improvements when setting up ciatah class.
• Added downloading of Gramm (https://github.com/piermorel/gramm) for graphics as external program.
• Updated to MIT license from GPL-3.0 License.

Example of movie slider and cell-extraction in the main GUI.

New functions

• None.

Updated @ciatah

• ciatahMainGui - Update to improve handling of output variables when figure closes to avoid calling invalid handles.
• computeCellDistances - Added gramm plots that show the distribution of cell-cell distances.
• getRegistrationSettings - Added support for certain options (e.g. motion correction) to give a vector and also added movie detrend options.
• modelPreprocessMovieFunction - Add support for multiple reference frames, the mean is taken before input to motion correction. Added support for detrending movies.
• ciatahMainGui - Add sliders to allow users to quickly scroll through both movies. Updated to ensure movie callback playback loop operations only occur if handles to movies are still valid, e.g. if main GUI figure is still open.

Updated ciapkg

• signalSorter - Changed call to overloaded functions to ciapkg.overloaded to avoid altering users Matlab workspace native functions. Change selection of cell on the maps to be instantaneous for where the mouse location is, much faster, don't have to wait for ginputCustom cross-hairs to show. Users can still show crosshairs with 'V'.
• thresholdImages - Fast border calculation using convn for options.fastThresholding==1, less precise than bwboundaries or bwareafilt but works for fast display purposes.
• manageMiji - Check that ImageJ already in java path to prevent duplicate loading and wasting time.

Updated +ciapkg

• `io.loadDependencies' - Added backup URL for downloading mij.jar.
• loadBatchFxns - Remove redundant loading and unloading of external programs via additional checks. Moved loadBatchFxns into ciapkg package. Use ciapkg.getDir to get directory as standard IO.
• startup - moved into ciapkg package.
• loadDependencies - Added gramm (https://github.com/piermorel/gramm) support/downloading for graphics plotting.

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This discussion was created from the release Updated to license, move functions into ciapkg package, gramm graphics, detrend support, speed improvements, movie controls to CIAtah main GUI, etc..