"""
default caiman parameters for lbm data processing.
"""
[docs]
def default_ops() -> dict:
"""
return default caiman parameters optimized for lbm microscopy data.
returns
-------
dict
dictionary of parameters for motion correction and cnmf.
"""
return {
# motion correction parameters
"do_motion_correction": True,
"max_shifts": (6, 6),
"strides": (48, 48),
"overlaps": (24, 24),
"max_deviation_rigid": 3,
"pw_rigid": True,
"gSig_filt": (2, 2),
"border_nan": "copy",
"niter_rig": 1,
"splits_rig": 14,
"num_splits_to_process_rig": None,
"splits_els": 14,
"num_splits_to_process_els": None,
"upsample_factor_grid": 4,
"max_deviation_rigid": 3,
"use_cuda": False,
# cnmf parameters
"do_cnmf": True,
"K": 50,
"gSig": (4, 4),
"gSiz": None,
"p": 1,
"merge_thresh": 0.8,
"min_SNR": 2.5,
"rval_thr": 0.85,
"decay_time": 0.4,
"method_init": "greedy_roi",
"ssub": 1,
"tsub": 1,
"rf": None,
"stride": None,
"nb": 1,
"gnb": 1,
"low_rank_background": True,
"update_background_components": True,
"rolling_sum": True,
"only_init": False,
"normalize_init": True,
"ring_size_factor": 1.5,
# component evaluation
"min_cnn_thr": 0.9,
"cnn_lowest": 0.1,
"use_cnn": False,
# general parameters
"fr": 30.0,
"n_processes": None,
"dxy": (1.0, 1.0),
}
[docs]
def mcorr_ops() -> dict:
"""return only motion correction parameters."""
ops = default_ops()
return {k: v for k, v in ops.items() if k in (
"do_motion_correction", "max_shifts", "strides", "overlaps",
"max_deviation_rigid", "pw_rigid", "gSig_filt", "border_nan",
"niter_rig", "splits_rig", "num_splits_to_process_rig",
"splits_els", "num_splits_to_process_els", "upsample_factor_grid",
"use_cuda", "fr", "n_processes", "dxy",
)}
[docs]
def cnmf_ops() -> dict:
"""return only cnmf parameters."""
ops = default_ops()
return {k: v for k, v in ops.items() if k in (
"do_cnmf", "K", "gSig", "gSiz", "p", "merge_thresh", "min_SNR",
"rval_thr", "decay_time", "method_init", "ssub", "tsub", "rf",
"stride", "nb", "gnb", "low_rank_background",
"update_background_components", "rolling_sum", "only_init",
"normalize_init", "ring_size_factor", "min_cnn_thr", "cnn_lowest",
"use_cnn", "fr", "n_processes", "dxy",
)}
