`CIAtah` functions within `ciapkg` sub-package.¶

CIAtah contains many functions for imaging analysis, from processing videos to wrappers for running cell extraction algorithms and GUIs for visualizing movies and evaluating cell extraction outputs. Several are detailed below. For each users can visualize options with help FUN or edit FUN. If attempting to load a non-package function (e.g. it does not start with ciapkg), then append ciapkg.api., e.g. playMovie would become ciapkg.api.playMovie. Alternatively, load all the functions into the workspace with import ciapkg.api.*.

This page will be further updated with information soon.

Visualizing movies¶

playMovie

ciapkg.io.loadMovie or loadMovieList

createImageOutlineOnMovie

createSignalBasedMovie

ciapkg.io.readFrame

Get movie information¶

ciapkg.io.getMovieInfo

Sorting cells¶

signalSorter

Pre-processing¶

ciapkg.demo.runPreprocessing

downsampleHdf5Movie

removeStripsFromMovie

turboregMovie

dfofMovie

downsampleMovie

normalizeMovie

Cell extraction¶

PCA-ICA - ciapkg.signal_extraction.runPcaIca.

Cross-session alignment¶

matchObjBtwnTrials

createMatchObjBtwnTrialsMaps

CIAtah functions within ciapkg sub-package.¶