CIAtah (pronounced cheetah): a software package for calcium imaging analysis of one- and two-photon imaging datasets. Documentation: https://git.io/ciatah_docs. Formerly known as calciumImagingAnalysis (ciapkg).
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.
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.
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.
Main features and changes:
New functions
ciapkg.io.getOptions
- clone ofgetOptions
in anticipation of moving all functions tociapkg
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
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.