Index

_

__init__() (caiman.source_extraction.cnmf.params.CNMFParams method) (caiman.source_extraction.volpy.volparams.volparams method) (caiman.source_extraction.volpy.volpy.VOLPY method)

A

Additive (class in caiman.utils.nn_models)

apply_shifts_movie() (caiman.motion_correction.MotionCorrect method) apply_to_patch() (in module caiman.cluster)

C

change_params() (caiman.source_extraction.cnmf.params.CNMFParams method) (caiman.source_extraction.volpy.volparams.volparams method) CNMF (class in caiman.source_extraction.cnmf.cnmf) CNMFParams (class in caiman.source_extraction.cnmf.params) com() (in module caiman.base.rois) compute_residuals() (caiman.source_extraction.cnmf.cnmf.CNMF method) (caiman.source_extraction.cnmf.estimates.Estimates method)

computeDFF() (caiman.base.movies.movie method) constrained_foopsi() (in module caiman.source_extraction.cnmf.deconvolution) constrained_oasisAR2() (in module caiman.source_extraction.cnmf.deconvolution) correlation_pnr() (in module caiman.summary_images) create_LN_model() (in module caiman.utils.nn_models)

D

deconvolve() (caiman.source_extraction.cnmf.cnmf.CNMF method) (caiman.source_extraction.cnmf.estimates.Estimates method)

detrend_df_f() (caiman.source_extraction.cnmf.estimates.Estimates method) (in module caiman.source_extraction.cnmf.utilities)

E

Estimates (class in caiman.source_extraction.cnmf.estimates) evaluate_components() (caiman.source_extraction.cnmf.estimates.Estimates method)

evaluate_components_CNN() (caiman.source_extraction.cnmf.estimates.Estimates method) extract_binary_masks_from_structural_channel() (in module caiman.base.rois)

F

filter_components() (caiman.source_extraction.cnmf.estimates.Estimates method) fit() (caiman.source_extraction.cnmf.cnmf.CNMF method) (caiman.source_extraction.volpy.volpy.VOLPY method)

fit_file() (caiman.source_extraction.cnmf.cnmf.CNMF method) fit_next() (caiman.source_extraction.cnmf.online_cnmf.OnACID method) fit_NL_model() (in module caiman.utils.nn_models) fit_online() (caiman.source_extraction.cnmf.online_cnmf.OnACID method)

G

get() (caiman.source_extraction.cnmf.params.CNMFParams method) (caiman.source_extraction.volpy.volparams.volparams method) get_file_size() (in module caiman.source_extraction.cnmf.utilities) get_group() (caiman.source_extraction.cnmf.params.CNMFParams method) (caiman.source_extraction.volpy.volparams.volparams method)

graphNMF() (in module caiman.source_extraction.cnmf.initialization) greedyROI() (in module caiman.source_extraction.cnmf.initialization) greedyROI_corr() (in module caiman.source_extraction.cnmf.initialization)

H

Hadamard (class in caiman.utils.nn_models) HALS4footprints() (caiman.source_extraction.cnmf.cnmf.CNMF method)

HALS4traces() (caiman.source_extraction.cnmf.cnmf.CNMF method) hv_view_components() (caiman.source_extraction.cnmf.estimates.Estimates method)

I

initialize() (caiman.source_extraction.cnmf.cnmf.CNMF method)

initialize_components() (in module caiman.source_extraction.cnmf.initialization) initialize_online() (caiman.source_extraction.cnmf.online_cnmf.OnACID method)

L

load() (in module caiman.base.movies) load_CNMF() (in module caiman.source_extraction.cnmf.cnmf) load_memmap() (in module caiman.mmapping)

load_movie_chain() (in module caiman.base.movies) load_OnlineCNMF() (in module caiman.source_extraction.cnmf.online_cnmf) local_correlations() (in module caiman.summary_images)

M

Masked_Conv2D (class in caiman.utils.nn_models) max_correlation_image() (in module caiman.summary_images) merge_components() (in module caiman.source_extraction.cnmf.merging) merge_comps() (caiman.source_extraction.cnmf.cnmf.CNMF method)

motion_correct() (caiman.motion_correction.MotionCorrect method) motion_correct_pwrigid() (caiman.motion_correction.MotionCorrect method) motion_correct_rigid() (caiman.motion_correction.MotionCorrect method) MotionCorrect (class in caiman.motion_correction) movie (class in caiman.base.movies)

N

nb_view_components() (caiman.source_extraction.cnmf.estimates.Estimates method)

nb_view_components_3d() (caiman.source_extraction.cnmf.estimates.Estimates method) normalize_components() (caiman.source_extraction.cnmf.estimates.Estimates method)

O

OnACID (class in caiman.source_extraction.cnmf.online_cnmf)

P

play() (caiman.base.movies.movie method) play_movie() (caiman.source_extraction.cnmf.estimates.Estimates method) plot_contours() (caiman.source_extraction.cnmf.estimates.Estimates method)

plot_contours_nb() (caiman.source_extraction.cnmf.estimates.Estimates method) preprocess() (caiman.source_extraction.cnmf.cnmf.CNMF method) preprocess_data() (in module caiman.source_extraction.cnmf.pre_processing)

Q

quantile_loss() (in module caiman.utils.nn_models)

R

refit() (caiman.source_extraction.cnmf.cnmf.CNMF method) register_multisession() (in module caiman.base.rois) register_ROIs() (in module caiman.base.rois) remove_components() (caiman.source_extraction.cnmf.cnmf.CNMF method)

remove_duplicates() (caiman.source_extraction.cnmf.estimates.Estimates method) remove_small_large_neurons() (caiman.source_extraction.cnmf.estimates.Estimates method) resize() (caiman.base.movies.movie method) restore_discarded_components() (caiman.source_extraction.cnmf.estimates.Estimates method)

S

save() (caiman.base.timeseries.timeseries method) (caiman.source_extraction.cnmf.cnmf.CNMF method) (caiman.source_extraction.cnmf.online_cnmf.OnACID method) save_memmap() (in module caiman.mmapping) save_memmap_join() (in module caiman.mmapping) save_NWB() (caiman.source_extraction.cnmf.estimates.Estimates method)

select_components() (caiman.source_extraction.cnmf.estimates.Estimates method) set() (caiman.source_extraction.cnmf.params.CNMFParams method) (caiman.source_extraction.volpy.volparams.volparams method) sparseNMF() (in module caiman.source_extraction.cnmf.initialization) start_server() (in module caiman.cluster) stop_server() (in module caiman.cluster)

T

timeseries (class in caiman.base.timeseries)

to_dict() (caiman.source_extraction.cnmf.params.CNMFParams method)

U

update_order() (in module caiman.source_extraction.cnmf.utilities) update_spatial() (caiman.source_extraction.cnmf.cnmf.CNMF method)

update_spatial_components() (in module caiman.source_extraction.cnmf.spatial) update_temporal() (caiman.source_extraction.cnmf.cnmf.CNMF method) update_temporal_components() (in module caiman.source_extraction.cnmf.temporal)

V

view_components() (caiman.source_extraction.cnmf.estimates.Estimates method) volparams (class in caiman.source_extraction.volpy.volparams)

VOLPY (class in caiman.source_extraction.volpy.volpy) volspike() (in module caiman.source_extraction.volpy.spikepursuit)