kandimallaprat / avppol_elife2021 Goto Github PK

Two-photon calcium imaging analysis code for investigation of polarization-sensitive neurons in the Drosophila anterior visual pathway (AVP)

Corresponding data can be found in the project repository at the Open Science Framework.

Matlab object classes with core functions for analysis of tiff files:

• SlidebookObj

  Superclass, one object per tiff file.
  Provides base functions for avp4DmaxObj - not used directly.
  Additional documentation: github.com/bjhardcastle

• avp4DmaxObj

  Subclass of SlidebookObj for polarization experiments.
  One object per tiff file (single imaging plane or max intensity projection).

• avp4DsuperObj

  Independent class for groups of associated avp4DmaxObj
  One object per recording.
  Contains multiple objects:

  • active channel (GCaMP)
    • MIP (single avp4DmaxObj)
    • individual layers from stack ([1xN] avp4DmaxObj array)
  • static channel (tdTomato)
    • MIP (single avp4DmaxObj)
    • individual layers from stack ([1xN] avp4DmaxObj array)

• /additionalfuncs, /icons

  Extra functions for plotting or viewing data, many third-party, including modified version of James Strother's Neuron Image Analysis GUI for playback of tiff files: bitbucket.com/jastrother

• /load_object_functions

  Loads .mat files in objarrays along with some additional variables/processing.

• /make_figure_panels

  Scripts for running analysis and printing plots.

• /plotting

  General functions for visualizing data or specific scripts to generate one-off plots.

• /refresh

  Scripts to re-analyze and store .mat files in /mat/plotting/

Convert polarizer angles as-recorded to convetion used in publication: wrapTo180(-theta-270)