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Improved pre-processing UI, Bio-Formats support, easier ImageJ/Miji loading, and more.
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@bahanonu bahanonu released this 22 Jun 04:20
· 101 commits to master since this release
v3.30.1
a60e749
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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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