Improved pre-processing UI, Bio-Formats support, easier ImageJ/Miji loading, and more.

[bahanonu]

Main features and changes:

• modelPreprocessMovieFunction - CIAtah now remembers the user's analysis order and there are options to reset it. Further, the pre-processing settings are now all displayed on a single page.
• Bio-Formats (https://www.openmicroscopy.org/bio-formats/) support added. Currently added support for Zeiss (CZI, LSM) and Olympus (OIR) formats with more to follow.
• Switch support from Miji/Fiji combination to ImageJ/Miji combination using .jar files that is easier to install and should have easier support across Windows/Linux/OSX.
• Update README to include webinars and workshop recordings on calcium imaging analysis and CIAtah.

New functions

• ciapkg.io.getOptions - clone of getOptions in anticipation of moving all functions to ciapkg sub-package.
• @ciatah\modelVarsFromFilesCheck - Checks whether a specific folder has cell extraction variables loaded, if not loads them.

Updated @ciatah

• computeManualSortSignals - Added modelVarsFromFilesCheck() to check and load signals if user hasn't already. Fix check to make sure variables are loaded.
• computeMatchObjBtwnTrials - Added modelVarsFromFilesCheck() to check and load signals if user hasn't already.
• getRegistrationSettings - Switch to single page support. Multi-column layout since most computers are widescreen now.
• modelExtractSignalsFromMovie - Use filesep in getAlgorithmRootPath to avoid issues in Unix-based systems. Fix issue of passing multiple movies to PCA-ICA.
• modelModifyMovies - manageMiji('startStop','closeAllWindows'); added to improve support for ImageJ over Fiji implementation of Miji.
• modelModifyRegionAnalysis - Added modelVarsFromFilesCheck() to check and load signals if user hasn't already.
• modelPreprocessMovieFunction
  • Fixed thisFrame issue when displaying area to use for motion correction if treatMoviesAsContinuous=0 and processMoviesSeparately=0, e.g. would load reference frame from each and if there were 3 movies, would assume RGB, causing display to be white.
  • Also update so the display frame takes into account custom frame list range. Updated checking of options. Also save ordering of options selected.
  • Added manageMiji('startStop','closeAllWindows'); support.
• modelVarsFromFilesCheck - Add check for objLocations.
• viewCellExtractionOnMovie - Added modelVarsFromFilesCheck() to check and load signals if user hasn't already.
• viewCreateObjmaps - Added modelVarsFromFilesCheck() to check and load signals if user hasn't already.
• viewMovie - Added support for simple and advanced settings. Added modelVarsFromFilesCheck() to check and load signals if user hasn't already.
• viewMovieRegistrationTest - Added modelVarsFromFilesCheck() to check and load signals if user hasn't already.
• viewObjmaps - Added modelVarsFromFilesCheck() to check and load signals if user hasn't already.
• viewSubjectMovieFrames - Added modelVarsFromFilesCheck() to check and load signals if user hasn't already.

Updated ciapkg

• signalSorter - Since ciapkg.io.loadSignalExtraction already supports loading NWB or CIAtah MAT-file cell extraction files, remove remove redundancy and only call ciapkg.io.loadSignalExtraction rather than loadNeurodataWithoutBorders. Added support for progress bar when movie not input.
• cropMatrix - Support switched from [nSignals x y] to [x y nSignals]. Updated to make imrect the default method of selecting the coordinates.
• loadMovieList - Added support for Bio-Formats compatible files, specifically Olympus (OIR) and Zeiss (CZI, LSM).
• manageMiji - Add support for setting up ImageJ along with closing all windows to future proof any changes to those calls.
• modelAddOutsideDependencies - Updated to add support for ImageJ call instead of Fiji.
• saveMatrixToFile - updated TIFF saving to add support for export of multi-channel color timeseries TIFF stack if in format [x y C t] where x,y = width/height, C = RGB channels, t = frames.
• computeManualMotionCorrection - Add default gamma option. Update to fix issue of prior figure (even after clf) maintaining previous key press and exiting, causing uiwait to fail.
• normalizeMovie - Detrend movie now uses nanmean to get around issues in motion corrected videos.
• createMovieFromVector - Users can now manually change value assigned to center line or signal.
• playMovie - Add support for playing RGB movie of dimension [x y C t] if input directly as matrix.
• loadBatchFxns - Added manageMiji('startStop','closeAllWindows'); support.

Updated +ciapkg

• cmdLinePipeline - Added CNMF/CNMF-e and EXTRACT to cell extraction examples.
• loadDependencies - Switched to support for original MIJ calling of ImageJ using just jar files, easier compatibility across MATLAB versions and OSes.
• updatePkg - Added additional URLs for compatibility. Updated to ciatah from calciumImagingAnalysis URLs.

Misc

• ciapkg.io.updatePkg - option on whether to update package (only 0 for now). Also alert user if behind a version.
• ciapkgRoot moved into +ciapkg folder.
• ciapkg.version - Update VERSION path.
• ciapkg.versionOnline - Update VERSION path.
• plotSignalsGraph - Fix minIncrementAmount issue.
• • ciapkg.versionOnline - Now checks multiple location of VERSION file to future proof in case it is moved.
• ciatah - checks online for version at startup.
• ciapkg.nwb.setupNwb - Fix for options.defaultObjDir leading to incorrect NWB folder and cores not being generated.

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