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).
Added detrend support for ciatah class modelPreprocessMovieFunction.
Moved ciapkg overloaded functions into sub-package ciapkg.overloaded to clean up namespace and not interfere with users namespace, updated dependent functions accordingly.
Moved startup into ciapkg to prevent changing user settings at startup.
Moved loadBatchFxns into ciapkg package and updated all functions accordingly.
ciatahMainGui - Update to improve handling of output variables when figure closes to avoid calling invalid handles.
computeCellDistances - Added gramm plots that show the distribution of cell-cell distances.
getRegistrationSettings - Added support for certain options (e.g. motion correction) to give a vector and also added movie detrend options.
modelPreprocessMovieFunction - Add support for multiple reference frames, the mean is taken before input to motion correction. Added support for detrending movies.
Updated ciapkg
signalSorter - Changed call to overloaded functions to ciapkg.overloaded to avoid altering users Matlab workspace native functions. Change selection of cell on the maps to be instantaneous for where the mouse location is, much faster, don't have to wait for ginputCustom cross-hairs to show. Users can still show crosshairs with 'V'.
thresholdImages - Fast border calculation using convn for options.fastThresholding==1, less precise than bwboundaries or bwareafilt but works for fast display purposes.
manageMiji - Check that ImageJ already in java path to prevent duplicate loading and wasting time.
Updated +ciapkg
loadBatchFxns - Remove redundant loading and unloading of external programs via additional checks. Moved loadBatchFxns into ciapkg package. Use ciapkg.getDir to get directory as standard IO.
Main features and changes:
ciatah
class modelPreprocessMovieFunction.ciapkg
overloaded functions into sub-packageciapkg.overloaded
to clean up namespace and not interfere with users namespace, updated dependent functions accordingly.startup
intociapkg
to prevent changing user settings at startup.loadBatchFxns
intociapkg
package and updated all functions accordingly.ciatah
class.New functions
Updated
@ciatah
ciatahMainGui
- Update to improve handling of output variables when figure closes to avoid calling invalid handles.computeCellDistances
- Added gramm plots that show the distribution of cell-cell distances.getRegistrationSettings
- Added support for certain options (e.g. motion correction) to give a vector and also added movie detrend options.modelPreprocessMovieFunction
- Add support for multiple reference frames, the mean is taken before input to motion correction. Added support for detrending movies.Updated
ciapkg
signalSorter
- Changed call to overloaded functions tociapkg.overloaded
to avoid altering users Matlab workspace native functions. Change selection of cell on the maps to be instantaneous for where the mouse location is, much faster, don't have to wait for ginputCustom cross-hairs to show. Users can still show crosshairs with 'V'.thresholdImages
- Fast border calculation using convn for options.fastThresholding==1, less precise than bwboundaries or bwareafilt but works for fast display purposes.manageMiji
- Check that ImageJ already in java path to prevent duplicate loading and wasting time.Updated
+ciapkg
loadBatchFxns
- Remove redundant loading and unloading of external programs via additional checks. Moved loadBatchFxns into ciapkg package. Use ciapkg.getDir to get directory as standard IO.startup
- moved intociapkg
package.loadDependencies
- Added gramm (https://github.com/piermorel/gramm) support/downloading for graphics plotting.