Index

A

add_roi_data() (siffpy.core.utils.im_params.im_params.ImParams method) align_reference_frames() (siffpy.core.utils.registration_tools.siffpy.SiffpyRegistrationInfo method) align_to_reference() (siffpy.core.utils.registration_tools.registration_info.RegistrationInfo method) (siffpy.core.utils.registration_tools.siffpy.SiffpyRegistrationInfo method) (siffpy.core.utils.registration_tools.suite2p.Suite2pRegistrationInfo method) all_frames (siffpy.core.utils.im_params.im_params.ImParams property)

allow_noise (siffpy.core.flim.flimparams.FLIMParams property) array_shape (siffpy.core.utils.im_params.im_params.ImParams property) arrival_time_bins (siffpy.core.utils.im_params.im_params.ImParams property) as_units() (siffpy.core.flim.flimparams.FLIMParams method) assign_siffio() (siffpy.core.utils.registration_tools.registration_info.RegistrationInfo method) Average (siffpy.core.utils.registration_tools.registration_info.RegistrationType attribute) axis_labels (siffpy.core.utils.im_params.im_params.ImParams property)

B

backend (siffpy.core.utils.registration_tools.registration_info.RegistrationInfo attribute) (siffpy.core.utils.registration_tools.siffpy.SiffpyRegistrationInfo attribute) (siffpy.core.utils.registration_tools.suite2p.Suite2pRegistrationInfo attribute)

bounds (siffpy.core.flim.flimparams.FLIMParams property) (siffpy.core.flim.multi_pulse.MultiPulseFLIMParams property)

C

Caiman (siffpy.core.utils.registration_tools.registration_info.RegistrationType attribute) CHANNEL_AXIS (siffpy.core.utils.im_params.im_params.ImParams attribute) close() (siffpy.core.siffreader.SiffReader method) (siffreadermodule.SiffIO method) color_list (siffpy.core.utils.im_params.im_params.ImParams property) colors (siffpy.core.utils.im_params.im_params.ImParams property)

constraints (siffpy.core.flim.flimparams.FLIMParams property) (siffpy.core.flim.multi_pulse.MultiPulseFLIMParams property) conversion_factor() (siffpy.core.flim.flimunits.FlimUnits method) convert_flimunits() (siffpy.core.flim.flimunits.FlimUnits static method) convert_units() (siffpy.core.flim.flimparams.FLIMParameter method) (siffpy.core.flim.flimparams.FLIMParams method) (siffpy.siffmath.flim.traces.FlimTrace method)

D

debug (siffreadermodule.SiffIO attribute) discard_frames (siffpy.core.utils.im_params.im_params.ImParams property)

dt_frame (siffpy.core.siffreader.SiffReader property) dt_volume (siffpy.core.siffreader.SiffReader property)

E

epoch_to_frame_time() (siffpy.core.siffreader.SiffReader method)

excludes_func() (siffpy.siffmath.flim.traces.FlimTrace class method) excludes_ufunc() (siffpy.siffmath.flim.traces.FlimTrace class method)

F

filename (siffreadermodule.SiffIO attribute) final_full_volume_frame (siffpy.core.utils.im_params.im_params.ImParams property) fit_params_to_data() (siffpy.core.flim.flimparams.FLIMParams method) (siffpy.core.flim.multi_pulse.MultiPulseFLIMParams method) flatten_by_timepoints() (siffpy.core.utils.im_params.im_params.ImParams method) flim_map() (siffreadermodule.SiffIO method) flim_params (siffpy.core.siffreader.SiffReader property) FLIMParameter (class in siffpy.core.flim.flimparams) FLIMParams (class in siffpy.core.flim.flimparams) FlimTrace (class in siffpy.siffmath.flim.traces) FlimUnits (class in siffpy.core.flim.flimunits) fluorescence (siffpy.siffmath.flim.traces.FlimTrace property) FluorescenceTrace (class in siffpy.siffmath.fluorescence.traces) FluorescenceVector (class in siffpy.siffmath.fluorescence.traces) flyback_frames (siffpy.core.utils.im_params.im_params.ImParams property)

fraction_bounds (siffpy.core.flim.flimparams.FLIMParams property) fraction_constraints (siffpy.core.flim.flimparams.FLIMParams property) frame_time_to_epoch_time() (siffpy.core.siffreader.SiffReader method) framelist_by_color() (siffpy.core.utils.im_params.im_params.ImParams method) framelist_by_slice() (siffpy.core.utils.im_params.im_params.ImParams method) framelist_by_slices() (siffpy.core.utils.im_params.im_params.ImParams method) framelist_by_timepoint() (siffpy.core.utils.im_params.im_params.ImParams method) frames_per_slice (siffpy.core.utils.im_params.im_params.ImParams property) frames_per_volume (siffpy.core.utils.im_params.im_params.ImParams property) from_dict() (siffpy.core.flim.flimparams.FLIMParameter class method) (siffpy.core.flim.flimparams.FLIMParams class method) (siffpy.core.flim.multi_pulse.MultiPulseFLIMParams class method) (siffpy.core.utils.im_params.im_params.ImParams static method) (siffpy.core.utils.registration_tools.registration_info.RegistrationInfo method) from_tuple() (siffpy.core.flim.flimparams.FLIMParams class method) (siffpy.core.flim.multi_pulse.MultiPulseFLIMParams class method)

G

get_appended_text() (siffpy.core.siffreader.SiffReader method) (siffreadermodule.SiffIO method) get_epoch_both() (siffreadermodule.SiffIO method) get_epoch_timestamps_laser() (siffreadermodule.SiffIO method) get_epoch_timestamps_system() (siffreadermodule.SiffIO method) get_experiment_timestamps() (siffreadermodule.SiffIO method) get_file_header() (siffreadermodule.SiffIO method)

get_frame_metadata() (siffreadermodule.SiffIO method) get_frames() (siffpy.core.siffreader.SiffReader method) (siffreadermodule.SiffIO method) get_frames_flim() (siffpy.core.siffreader.SiffReader method) get_histogram() (siffpy.core.siffreader.SiffReader method) (siffreadermodule.SiffIO method) get_time() (siffpy.core.siffreader.SiffReader method)

H

histograms() (siffpy.core.siffreader.SiffReader method)

I

imaging_fov (siffpy.core.utils.im_params.im_params.ImParams property) ImParams (class in siffpy.core.utils.im_params.im_params) implements_func() (siffpy.siffmath.flim.traces.FlimTrace class method)

implements_ufunc() (siffpy.siffmath.flim.traces.FlimTrace class method) irfs (siffpy.core.flim.multi_pulse.MultiPulseFLIMParams property) items() (siffpy.core.utils.im_params.im_params.ImParams method)

K

keys() (siffpy.core.utils.im_params.im_params.ImParams method)

L

lifetime (siffpy.siffmath.flim.traces.FlimTrace property) load() (siffpy.core.flim.flimparams.FLIMParams class method) (siffpy.siffmath.flim.traces.FlimTrace class method) (siffpy.siffmath.fluorescence.traces.FluorescenceTrace class method)

load_as_dict() (siffpy.core.utils.registration_tools.registration_info.RegistrationInfo class method) load_time_axis() (siffpy.core.siffreader.SiffReader class method) lowest_color_channel (siffpy.core.utils.im_params.im_params.ImParams property)

M

mean() (siffpy.siffmath.flim.traces.FlimTrace method) module siffpy.core.siffreader siffreadermodule

MultiPulseFLIMParams (class in siffpy.core.flim.multi_pulse) multithreading_compatible (siffpy.core.utils.registration_tools.registration_info.RegistrationInfo attribute) (siffpy.core.utils.registration_tools.siffpy.SiffpyRegistrationInfo attribute) (siffpy.core.utils.registration_tools.suite2p.Suite2pRegistrationInfo attribute)

N

n_exp (siffpy.core.flim.flimparams.FLIMParams property) n_params (siffpy.core.flim.multi_pulse.MultiPulseFLIMParams property) n_pulses (siffpy.core.flim.multi_pulse.MultiPulseFLIMParams property) ncomponents (siffpy.core.flim.flimparams.FLIMParams property) noise (siffpy.core.flim.flimparams.FLIMParams property) nondimensionalize() (siffpy.core.flim.flimparams.FLIMParameter method) num_bins (siffpy.core.utils.im_params.im_params.ImParams property)

num_colors (siffpy.core.utils.im_params.im_params.ImParams property) num_discard_flyback_frames (siffpy.core.utils.im_params.im_params.ImParams property) num_frames (siffpy.core.utils.im_params.im_params.ImParams property) num_frames() (siffreadermodule.SiffIO method) num_slices (siffpy.core.utils.im_params.im_params.ImParams property) num_timepoints (siffpy.core.utils.im_params.im_params.ImParams property) num_true_frames (siffpy.core.utils.im_params.im_params.ImParams property) num_volumes (siffpy.core.utils.im_params.im_params.ImParams property)

O

open() (siffpy.core.siffreader.SiffReader method) (siffreadermodule.SiffIO method)

Other (siffpy.core.utils.registration_tools.registration_info.RegistrationType attribute)

P

param_tuple (siffpy.core.flim.flimparams.FLIMParams property) (siffpy.core.flim.multi_pulse.MultiPulseFLIMParams property) params (siffpy.core.flim.flimparams.FLIMParams property) pdf() (siffpy.core.flim.flimparams.FLIMParams method) (siffpy.core.flim.multi_pulse.MultiPulseFLIMParams method)

picoseconds_per_bin (siffpy.core.utils.im_params.im_params.ImParams property) pool_frames() (siffpy.core.siffreader.SiffReader method) (siffreadermodule.SiffIO method) probability_dist() (siffpy.core.flim.flimparams.FLIMParams method) (siffpy.core.flim.multi_pulse.MultiPulseFLIMParams method)

R

ravel() (siffpy.siffmath.flim.traces.FlimTrace method) redimensionalize() (siffpy.core.flim.flimparams.FLIMParameter method) register() (siffpy.core.siffreader.SiffReader method), [1] (siffpy.core.utils.registration_tools.registration_info.RegistrationInfo method) (siffpy.core.utils.registration_tools.siffpy.SiffpyRegistrationInfo method) (siffpy.core.utils.registration_tools.suite2p.Suite2pRegistrationInfo method)

REGISTRATION_INFO_SUFFIX (siffpy.core.utils.registration_tools.registration_info.RegistrationInfo attribute) registration_params (siffpy.core.utils.registration_tools.suite2p.Suite2pRegistrationInfo attribute) registration_type (siffpy.core.utils.registration_tools.registration_info.RegistrationInfo property) RegistrationInfo (class in siffpy.core.utils.registration_tools.registration_info) RegistrationType (class in siffpy.core.utils.registration_tools.registration_info) reshape() (siffpy.siffmath.flim.traces.FlimTrace method)

S

sample() (siffpy.core.flim.flimparams.FLIMParams method) save() (siffpy.core.flim.flimparams.FLIMParams method) (siffpy.core.utils.registration_tools.registration_info.RegistrationInfo method) save_time_axis() (siffpy.core.siffreader.SiffReader method) scale (siffpy.core.utils.im_params.im_params.ImParams property) scale_force_z (siffpy.core.utils.im_params.im_params.ImParams property) scale_no_color_no_fps (siffpy.core.utils.im_params.im_params.ImParams property) sec_to_frames() (siffpy.core.siffreader.SiffReader method) series_shape (siffpy.core.siffreader.SiffReader property) set_units() (siffpy.siffmath.flim.traces.FlimTrace method) shape (siffpy.core.utils.im_params.im_params.ImParams property) siff_to_tiff() (in module siffpy) (in module siffreadermodule) SiffIO (class in siffreadermodule) Siffpy (siffpy.core.utils.registration_tools.registration_info.RegistrationType attribute) siffpy.core.siffreader module SiffpyRegistrationInfo (class in siffpy.core.utils.registration_tools.siffpy) SiffReader (class in siffpy.core.siffreader), [1]

siffreadermodule module single_channel_volume (siffpy.core.utils.im_params.im_params.ImParams property) sort() (siffpy.siffmath.flim.traces.FlimTrace method) squeeze() (siffpy.siffmath.flim.traces.FlimTrace method) stack (siffpy.core.utils.im_params.im_params.ImParams property) status (siffreadermodule.SiffIO attribute) step_size (siffpy.core.utils.im_params.im_params.ImParams property) Suite2p (siffpy.core.utils.registration_tools.registration_info.RegistrationType attribute) Suite2pRegistrationInfo (class in siffpy.core.utils.registration_tools.suite2p) sum() (siffpy.siffmath.flim.traces.FlimTrace method) sum_mask() (siffpy.core.siffreader.SiffReader method) sum_mask_flim() (siffpy.core.siffreader.SiffReader method) sum_masks() (siffpy.core.siffreader.SiffReader method) sum_masks_flim() (siffpy.core.siffreader.SiffReader method) sum_roi() (siffreadermodule.SiffIO method) sum_roi_flim() (siffreadermodule.SiffIO method) sum_rois() (siffreadermodule.SiffIO method) sum_rois_flim() (siffreadermodule.SiffIO method)

T

t_axis() (siffpy.core.siffreader.SiffReader method) T_O (siffpy.core.flim.flimparams.FLIMParams property) time_zero (siffpy.core.siffreader.SiffReader property)

to_alpha() (siffpy.siffmath.flim.traces.FlimTrace method) to_dict() (siffpy.core.flim.flimparams.FLIMParameter method) (siffpy.core.flim.flimparams.FLIMParams method) transpose() (siffpy.siffmath.flim.traces.FlimTrace method)

V

values() (siffpy.core.utils.im_params.im_params.ImParams method)

volume (siffpy.core.utils.im_params.im_params.ImParams property) volume_one_color (siffpy.core.utils.im_params.im_params.ImParams property)

X

xsize (siffpy.core.utils.im_params.im_params.ImParams property)

Y

ysize (siffpy.core.utils.im_params.im_params.ImParams property)

Z

z_vals (siffpy.core.utils.im_params.im_params.ImParams property)

zoom (siffpy.core.utils.im_params.im_params.ImParams property)