Index

A

add_constant_edges() (in module phathom.segmentation.graphcuts) add_gradient_edges() (in module phathom.segmentation.graphcuts) add_terminal_edges() (in module phathom.segmentation.graphcuts)

augment() (in module phathom.registration.pcloud) augmented_matrix() (in module phathom.registration.pcloud) average_residual() (in module phathom.registration.pcloud)

B

box_slice_idx() (in module phathom.utils)

build_neighbors() (in module phathom.registration.pcloud)

C

calculate_image_dimensions() (in module phathom.registration.pcloud) check_distance() (in module phathom.registration.pcloud) check_prominence() (in module phathom.registration.pcloud) check_range() (in module phathom.test_helpers)

chunk_coordinates() (in module phathom.utils) chunk_dims() (in module phathom.utils) coord_mapping() (in module phathom.registration.pcloud) create_new_graph() (in module phathom.segmentation.graphcuts)

E

entropy() (in module phathom.segmentation.graphcuts)

estimate_affine() (in module phathom.registration.pcloud) extract_box() (in module phathom.utils)

F

feature_matching() (in module phathom.registration.pcloud) files_in_dir() (in module phathom.utils) find_nearest_T() (in module phathom.segmentation.graphcuts)

find_primes() (in module phathom.test_helpers) fit_poisson_mixture() (in module phathom.segmentation.graphcuts) flatten() (in module phathom.registration.pcloud)

G

generate_3d_image() (in module phathom.registration.pcloud) geometric_features() (in module phathom.registration.pcloud) geometric_hash() (in module phathom.registration.pcloud) get_chunk_index() (in module phathom.registration.pcloud)

get_nb_bins() (in module phathom.segmentation.graphcuts) get_nb_chunks() (in module phathom.registration.pcloud) gradient_penalty_lut() (in module phathom.segmentation.graphcuts) graph_cuts() (in module phathom.segmentation.graphcuts)

H

hist() (in module phathom.segmentation.graphcuts)

histogram_penalty() (in module phathom.segmentation.graphcuts) histogram_penalty_lut() (in module phathom.segmentation.graphcuts)

I

index_to_um_tup() (in module phathom.registration.pcloud)

information_gain() (in module phathom.segmentation.graphcuts) insert_box() (in module phathom.utils)

L

load_metadata() (in module phathom.utils)

M

main() (in module phathom.registration.pcloud)

make_dir() (in module phathom.utils) max_entropy() (in module phathom.segmentation.graphcuts)

N

ncc() (in module phathom.registration.pcloud)

P

parallel_graph_cuts() (in module phathom.segmentation.graphcuts) pcloud_density_registration() (in module phathom.registration.pcloud) pcloud_hist() (in module phathom.registration.pcloud) phathom (module) phathom.atlas (module) phathom.db (module) phathom.io (module) phathom.phenotype (module) phathom.preprocess (module) phathom.registration (module)

phathom.registration.pcloud (module) phathom.segmentation (module) phathom.segmentation.graphcuts (module) phathom.test_helpers (module) phathom.utils (module) pickle_load() (in module phathom.utils) pickle_save() (in module phathom.utils) pmap_chunks() (in module phathom.utils) poisson_pdf() (in module phathom.segmentation.graphcuts) prominence() (in module phathom.registration.pcloud)

R

radius_matching() (in module phathom.registration.pcloud) register_pts() (in module phathom.registration.pcloud)

rigid_transformation() (in module phathom.registration.pcloud) rotate() (in module phathom.registration.pcloud) rotation_matrix() (in module phathom.registration.pcloud)

S

SharedMemory (class in phathom.utils)

T

tifs_in_dir() (in module phathom.utils)

txn() (phathom.utils.SharedMemory method)

U

unflatten() (in module phathom.registration.pcloud)