Index

B

binarization() (in module megafish.process)

C

coordinates_decoded() (in module megafish.decode) copy_groups() (in module megafish.utils)

count_spots() (in module megafish.seqfish) count_summary() (in module megafish.seqfish) create_chunk_dataframe() (in module megafish.register)

D

dilation() (in module megafish.segment) divide_by_norm() (in module megafish.decode)

DoG_filter() (in module megafish.seqfish) dog_sds() (in module megafish.seqfish) dummy_shift_tile() (in module megafish.register)

F

fill_holes() (in module megafish.segment)

G

gaussian_blur() (in module megafish.process) gaussian_kernel() (in module megafish.decode) get_edges() (in module megafish.register) get_intensity() (in module megafish.seqif)

get_overlap() (in module megafish.register) get_round_cycle() (in module megafish.utils) get_tile_yx() (in module megafish.utils) grow_voronoi() (in module megafish.segment)

I

ims_cYXzyx() (in module megafish.load)

info_csv() (in module megafish.segment) intnensity_summary() (in module megafish.seqif)

L

label_edge() (in module megafish.segment) load() (in module megafish.tif)

local_maxima() (in module megafish.seqfish) local_maxima_footprint() (in module megafish.seqfish)

M

make_dirlist() (in module megafish.load) make_imagepath_cYX() (in module megafish.load) make_imagepath_cYX_from_dirlist() (in module megafish.load) make_pyramid() (in module megafish.view) mask_edge() (in module megafish.view) masking() (in module megafish.process) (in module megafish.segment) max_filter() (in module megafish.view) megafish module megafish.config module megafish.decode module megafish.load module megafish.napari module megafish.process module megafish.register module megafish.segment module megafish.seqfish module

megafish.seqif module megafish.tif module megafish.utils module megafish.view module merfish_prefilter() (in module megafish.decode) merge_groups() (in module megafish.segment) merge_shift_cYXyx() (in module megafish.register) merge_split_label() (in module megafish.segment) merge_to_one_group() (in module megafish.segment) module megafish megafish.config megafish.decode megafish.load megafish.napari megafish.process megafish.register megafish.segment megafish.seqfish megafish.seqif megafish.tif megafish.utils megafish.view

N

natural_sort() (in module megafish.utils) nearest_neighbor() (in module megafish.decode)

norm_value() (in module megafish.decode) normalize_groups() (in module megafish.segment)

P

projection() (in module megafish.process)

R

registered() (in module megafish.napari) registered_is() (in module megafish.napari) registration_cYXyx() (in module megafish.register)

registration_cYXyx_noref() (in module megafish.register) remove_edge_mask() (in module megafish.segment) repeat_cycle() (in module megafish.segment)

S

save() (in module megafish.tif) save_chunk() (in module megafish.tif) save_rgb() (in module megafish.tif) save_tile_montage() (in module megafish.tif) save_whole_image() (in module megafish.tif) scaled_mip() (in module megafish.segment) scaling() (in module megafish.decode) segment() (in module megafish.napari) select_by_intensity_sd() (in module megafish.seqfish) select_by_intensity_threshold() (in module megafish.seqfish) select_decoded() (in module megafish.decode)

select_slice() (in module megafish.segment) set_resource() (in module megafish.config) set_scheduler() (in module megafish.config) shift_cycle_cYXyx() (in module megafish.register) shift_tile_cYXyx() (in module megafish.register) show_resource() (in module megafish.config) skip_odd_cycle() (in module megafish.seqif) split_nnd() (in module megafish.decode) spot_coordinates() (in module megafish.seqfish) spot_intensity() (in module megafish.seqfish) stitched_ims() (in module megafish.load) stitched_tif() (in module megafish.load)

T

TCEP_subtraction() (in module megafish.seqif)

tif_cYXzyx() (in module megafish.load) tile_2d() (in module megafish.napari)

U

use_gpu() (in module megafish.config)

W

watershed_label() (in module megafish.segment)