Improved pre-processing UI, Bio-Formats support, easier ImageJ/Miji loading, and more. #74
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…oading, and more. 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. - `computeMatchObjBtwnTrials` - Added modelVarsFromFilesCheck() to check and load signals if user hasn't already. - `getRegistrationSettings` - Switch to single page support. - `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. - `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.
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Tested Windows 10 on MATLAB
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Main features and changes:
New functions
ciapkg.io.getOptions- clone ofgetOptionsin anticipation of moving all functions tociapkgsub-package.@ciatah\modelVarsFromFilesCheck- Checks whether a specific folder has cell extraction variables loaded, if not loads them.Updated
@ciatahcomputeManualSortSignals- 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.modelPreprocessMovieFunctionmodelVarsFromFilesCheck- 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
ciapkgsignalSorter- 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
+ciapkgcmdLinePipeline- 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.