Index

A

add_fit() (in module iaf.plot)

apply_rigid_transform() (in module iaf.reg)

B

binary_shrink() (in module iaf.morph.morphology_utils)

Blue (iaf.color.Color attribute)

C

calc_sse() (in module iaf.fit.metrics) calc_sse_weighed() (in module iaf.fit.metrics) channel_names (iaf.io.readers.HuygensHDF5Reader property) (iaf.io.readers.ImarisReader property) (iaf.io.readers.NikonND2Reader property)

cluster_by_distance() (in module iaf.cluster) Color (class in iaf.color) cube() (in module iaf.morph.strel_3d) Cyan (iaf.color.Color attribute)

D

download_file() (in module iaf.io.utils)

E

ellipsoid() (in module iaf.morph.strel_3d) estimate_object_sizes() (in module iaf.morph.watershed)

exponential_model() (in module iaf.fit.models) extends (iaf.io.readers.ImarisReader property)

F

filename (iaf.io.readers.HuygensHDF5Reader property) (iaf.io.readers.ImarisReader property) (iaf.io.readers.NikonND2Reader property)

fill_labeled_holes() (in module iaf.morph.morphology_utils) filter_labels_by_area() (in module iaf.morph.watershed) find_rigid_transform() (in module iaf.reg)

G

geometry (iaf.io.readers.NikonND2Reader property) get_hilo_cmap() (in module iaf.color) get_label_areas() (in module iaf.morph.watershed)

get_labels_cmap() (in module iaf.color) Gray (iaf.color.Color attribute) Green (iaf.color.Color attribute)

H

hdf5_dataset (iaf.io.readers.HuygensHDF5Reader property)

hist_bins() (in module iaf.stats) HuygensHDF5Reader (class in iaf.io.readers)

I

iaf module iaf.cluster module iaf.color module iaf.filter module iaf.fit module iaf.fit.metrics module iaf.fit.models module iaf.io module iaf.io.cast module iaf.io.readers module iaf.io.utils module iaf.morph module iaf.morph.morphology_utils module

iaf.morph.strel_3d module iaf.morph.watershed module iaf.notebook module iaf.plot module iaf.plot.utils module iaf.plot.validation module iaf.process module iaf.reg module iaf.stats module ideal_hist_bins() (in module iaf.stats) ImarisReader (class in iaf.io.readers) imshow() (in module iaf.plot) init_style() (in module iaf.notebook) is_local_maximum() (in module iaf.morph.morphology_utils) iter_axis (iaf.io.readers.NikonND2Reader property)

L

label_to_eroded_bw_mask() (in module iaf.morph.watershed) linear_model() (in module iaf.fit.models)

load() (iaf.io.readers.HuygensHDF5Reader method) (iaf.io.readers.ImarisReader method) logarithmic_model() (in module iaf.fit.models)

M

metadata (iaf.io.readers.HuygensHDF5Reader property) (iaf.io.readers.NikonND2Reader property) module iaf iaf.cluster iaf.color iaf.filter iaf.fit iaf.fit.metrics iaf.fit.models iaf.io iaf.io.cast iaf.io.readers iaf.io.utils iaf.morph iaf.morph.morphology_utils iaf.morph.strel_3d iaf.morph.watershed iaf.notebook iaf.plot iaf.plot.utils iaf.plot.validation iaf.process iaf.reg iaf.stats

multi_image_alignment() (in module iaf.reg)

N

NikonND2Reader (class in iaf.io.readers) num_channels (iaf.io.readers.HuygensHDF5Reader property) (iaf.io.readers.ImarisReader property) (iaf.io.readers.NikonND2Reader property) num_planes (iaf.io.readers.HuygensHDF5Reader property) (iaf.io.readers.ImarisReader property) (iaf.io.readers.NikonND2Reader property)

num_series (iaf.io.readers.NikonND2Reader property) num_timepoints (iaf.io.readers.HuygensHDF5Reader property) (iaf.io.readers.ImarisReader property) (iaf.io.readers.NikonND2Reader property)

O

Orange (iaf.color.Color attribute)

P

parallelepiped() (in module iaf.morph.strel_3d) plot_background_subtraction_control() (in module iaf.plot.validation) plot_data() (in module iaf.plot)

plot_parameter_search_1d() (in module iaf.plot.utils) plot_parameter_search_2d() (in module iaf.plot.utils) prepare_histogram() (in module iaf.stats)

R

r_squared() (in module iaf.fit.metrics) r_squared_adj() (in module iaf.fit.metrics)

raw_metadata (iaf.io.readers.NikonND2Reader property) Red (iaf.color.Color attribute) relabel() (in module iaf.morph.morphology_utils)

S

safe_to_uint16() (in module iaf.io.cast) safe_to_uint8() (in module iaf.io.cast) sample() (in module iaf.process) separate_neighboring_objects() (in module iaf.morph.watershed) set_rc_params() (in module iaf.notebook) show_labels() (in module iaf.plot)

size (iaf.io.readers.HuygensHDF5Reader property) (iaf.io.readers.ImarisReader property) sphere() (in module iaf.morph.strel_3d) square_root_model() (in module iaf.fit.models) std_filter() (in module iaf.filter) strel_disk() (in module iaf.morph.morphology_utils) subtract_background() (in module iaf.process)

T

tile() (in module iaf.process)

to_composite() (in module iaf.color) to_rgb() (in module iaf.color)

V

var_filter() (in module iaf.filter) voxel_sizes (iaf.io.readers.HuygensHDF5Reader property) (iaf.io.readers.ImarisReader property) (iaf.io.readers.NikonND2Reader property)

Y

Yellow (iaf.color.Color attribute)