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Cell Registration

Cell Registrar w/ROICaT

CRwROI Input

  • multSessSegStruc

CRwROI Output

  • json with cluster info (_cluster_info_ROICaT.json)
  • results dictionary (_results_ROICaT)
  • ROICaT rundata dictionary (_rundata_ROICaT)
  • json with CR_wROI parameters (CRwROIparams.json)
  • Figures (stored in /path/to/multSessSegStruc/_Figures_ROICaT)

CRwROI CLI

usage: cellRegistrar_wROICaT.py   [-h] [-p PATH] [-s2p SESS2PROCESS]
                                  [-sf SESSFOCUS] [-G USEGPU] [-v VERBOSE]

Run CellRegistar with ROICaT with command line arguments.

options:
  -h, --help            show this help message and exit
  -p PATH, --path PATH  Path to the data directory (e.g. /path/to/data).
                        Default will prompt user to choose path.
                        NOTE: Pick directory which holds session folders.
                              Do not pick/set a session folder.
  -s2p SESS2PROCESS, --sess2process SESS2PROCESS
                        List of sessions to process. Write in format '1,2,3', '1-3',
                        or '1,2-5' to select by specific session number.
                        Input all or ALL to process all eligible sessions that are
                        available within the set path.
                        Default will prompt user to choose.
  -sf SESSFOCUS, --sessFocus SESSFOCUS
                        Set number of sessions to analyze.
                        Default is None, which will analyze all sessions found within
                        multSessSegStruc.
  -G USEGPU, --useGPU USEGPU
                        Whether to use GPU for ROICaT functions. Default is True
  -v VERBOSE, --verbose VERBOSE
                        Whether to print verbose output for ROICaT functions.
                        Default is True

Cell Registrar Cluster Info Collater (CR_CI_collater)

CICOLL Input

  • json with cluster info (_cluster_info_ROICaT.json)

CICOLL Output

  • csv with cluster info for all subjects (/path/to/_MS_dir/~GroupData/ClusterInfo_all.csv)
  • csv with cluster info averages by group (/path/to/_MS_dir/~GroupData/ClusterInfo_means.csv)

CICOLL CLI

usage: CR_CI_collater.py [-h] [-p PATH] [-s2p SESS2PROCESS] [-4p FORPRES]

Run CellRegistrar Cluster Info Collater with command line arguments.

options:
  -h, --help            show this help message and exit
  -p PATH, --path PATH  Path to the data directory (e.g. /path/to/data).
                        Default will prompt user to choose path.
                        NOTE: Pick directory which holds session folders.
                              Do not pick/set a session folder.
  -s2p SESS2PROCESS, --sess2process SESS2PROCESS
                        List of sessions to process. Write in format '1,2,3', '1-3',
                        or '1,2-5' to select by specific session number.
                        Input all or ALL to process all eligible sessions that are
                        available within the set path.
                        Default will prompt user to choose.
  -4p FORPRES, --forPres FORPRES
                        Whether to export .svg for figures in addition to the usual
                        png output. Default is False.