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).
ciapkg.behavior.importDeepLabCutData (see prior pull request).
ciapkg.tracking.annotateOpenFieldParameters - Requests information on arena size and center area for open field analysis from circular or square arenas.
Updated @ciatah
ciatah - Add guiFoldersSelected, prior user selected folders kept on next call.
ciatahMainGui - List of files in selected folder now contain file dates. Folder are now sorted to appear first in the list. Get around error with incorrect filter for input images applied. Allow user to reset folders along with prior select folders stay selected on next reload of object.
Updated +ciapkg
'ciapkg.io.loadMovieList' - Added mp4 support. Update AVI support to do additional cdata checks. To reduce automatic conversion to double when reading HDF5 with largeMovieLoad=1 and a specific set of frames, force outputMovie default value to be single. This is made consistent across all image types, checks if float or not then re-initializes default outputMovie.
ciapkg.io.readFrame - Update AVI support to do additional cdata checks. Add support for reading multiple files if a character cell array of char vectors is given. Add bioformats passing arguments for loadMovieList as options.
ciapkg.view.playMovie - Add support for mp4 files. Add support for overlaying DeepLabCut markers on the movie (including with confidence measure). Users can change size of overlay markers. Change default colormap to gray. Added downsample (both type) support for extra movie, mirrors what happens in the 1st movie. Also improved downsampling when just subsampling by removing unnecessary calls to imresize. Improved tracking point handling to ensure in the correct axes and can turn off prior frame tracking. Better handling of quiver plots with tracking. Convert all nanmin/nanmax to 'omitnan' and (:) to [1 2 3 4] to ensure compatible with 3- and 4-d tensors. Additional Bio-Formats support.
ciapkg.view.changeFont - Update to handle legend, since use TextColor property instead of Color for text. Users can also put in a blank fontSize to avoid changing that property, can skip UI that would normally appear.
ciapkg.view.setFigureDefaults - Disable Matlab UI font size change for code and text, that is left to the user.
Main features and changes:
4.6.1
.New functions
ciapkg.behavior.importDeepLabCutData
(see prior pull request).ciapkg.tracking.annotateOpenFieldParameters
- Requests information on arena size and center area for open field analysis from circular or square arenas.Updated
@ciatah
ciatah
- Add guiFoldersSelected, prior user selected folders kept on next call.ciatahMainGui
- List of files in selected folder now contain file dates. Folder are now sorted to appear first in the list. Get around error with incorrect filter for input images applied. Allow user to reset folders along with prior select folders stay selected on next reload of object.Updated
+ciapkg
ciapkg.io.readFrame
- Update AVI support to do additional cdata checks. Add support for reading multiple files if a character cell array of char vectors is given. Add bioformats passing arguments for loadMovieList as options.ciapkg.io.loadDependencies
- Ensure display location of SlideBook6Reader.jar saving. Add success output.ciapkg.io.saveMatrixToFile
- Comment updates.ciapkg.view.playMovie
- Add support for mp4 files. Add support for overlaying DeepLabCut markers on the movie (including with confidence measure). Users can change size of overlay markers. Change default colormap to gray. Added downsample (both type) support for extra movie, mirrors what happens in the 1st movie. Also improved downsampling when just subsampling by removing unnecessary calls to imresize. Improved tracking point handling to ensure in the correct axes and can turn off prior frame tracking. Better handling of quiver plots with tracking. Convert all nanmin/nanmax to 'omitnan' and (:) to [1 2 3 4] to ensure compatible with 3- and 4-d tensors. Additional Bio-Formats support.ciapkg.view.changeFont
- Update to handle legend, since use TextColor property instead of Color for text. Users can also put in a blank fontSize to avoid changing that property, can skip UI that would normally appear.ciapkg.view.setFigureDefaults
- Disable Matlab UI font size change for code and text, that is left to the user.