Two pipelines are described in detail in Matlab live scripts: \Analysis_Pipeline\Local\ExVivo_InVivo_RegExVivo_InVivo_Reg.mlx and \Analysis_Pipeline\Local\2P_Img_Processing\TwoPhoton_Imaging_Processing_Pipeline.mlx

If Matlab is not available for you, you can open the html files for these pipelines: \Analysis_Pipeline\Local\ExVivo_InVivo_RegExVivo_InVivo_Reg.html and \Analysis_Pipeline\Local\2P_Img_Processing\TwoPhoton_Imaging_Processing_Pipeline.html

Data_Set subfolder contains the preprocessed data of our CaRMA imaging and FISH-only.

Example_Data provides a link to our example data, which is stored in dropbox and will move to a share research data repository in the near future.