Index

_

_build_dask_array() (pymif.microscope_manager.luxendo_manager.LuxendoManager method) (pymif.microscope_manager.LuxendoManager method) (pymif.microscope_manager.opera_manager.OperaManager method) (pymif.microscope_manager.OperaManager method) (pymif.microscope_manager.viventis_manager.ViventisManager method) (pymif.microscope_manager.ViventisManager method) _generate_pyramid() (in module pymif.microscope_manager.utils.write_image_region) (in module pymif.microscope_manager.utils.write_label_region) _load_group() (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method) _load_labels() (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method) _open_files (pymif.microscope_manager.luxendo_manager.LuxendoManager attribute) (pymif.microscope_manager.LuxendoManager attribute) (pymif.microscope_manager.microscope_manager.MicroscopeManager attribute) _parse_color() (in module pymif.microscope_manager.utils.visualize) _parse_companion_file() (pymif.microscope_manager.viventis_manager.ViventisManager method) (pymif.microscope_manager.ViventisManager method)

_parse_metadata() (pymif.microscope_manager.luxendo_manager.LuxendoManager method) (pymif.microscope_manager.LuxendoManager method) (pymif.microscope_manager.opera_manager.OperaManager method) (pymif.microscope_manager.OperaManager method) (pymif.microscope_manager.zeiss_manager.ZeissManager method) (pymif.microscope_manager.ZeissManager method) _read_h5_shape() (pymif.microscope_manager.luxendo_manager.LuxendoManager method) (pymif.microscope_manager.LuxendoManager method) _read_h5_stack() (pymif.microscope_manager.luxendo_manager.LuxendoManager method) (pymif.microscope_manager.LuxendoManager method) _scale_index() (in module pymif.microscope_manager.utils.write_image_region) (in module pymif.microscope_manager.utils.write_label_region) _zoom_dask() (in module pymif.microscope_manager.utils.write_image_region) (in module pymif.microscope_manager.utils.write_label_region) _zoom_numpy() (in module pymif.microscope_manager.utils.write_image_region) (in module pymif.microscope_manager.utils.write_label_region)

A

add_label() (in module pymif.microscope_manager.utils.add_label) (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method)

ArrayManager (class in pymif.microscope_manager) (class in pymif.microscope_manager.array_manager)

B

build_pyramid() (in module pymif.microscope_manager.utils.pyramid) (pymif.microscope_manager.microscope_manager.MicroscopeManager method)

C

chunks (pymif.microscope_manager.array_manager.ArrayManager attribute) (pymif.microscope_manager.ArrayManager attribute) (pymif.microscope_manager.luxendo_manager.LuxendoManager attribute) (pymif.microscope_manager.LuxendoManager attribute) (pymif.microscope_manager.opera_manager.OperaManager attribute) (pymif.microscope_manager.OperaManager attribute) (pymif.microscope_manager.viventis_manager.ViventisManager attribute) (pymif.microscope_manager.ViventisManager attribute) (pymif.microscope_manager.zarr_manager.ZarrManager attribute) (pymif.microscope_manager.ZarrManager attribute) (pymif.microscope_manager.zeiss_manager.ZeissManager attribute) (pymif.microscope_manager.ZeissManager attribute)

close() (pymif.microscope_manager.microscope_manager.MicroscopeManager method) create_empty_dataset() (in module pymif.microscope_manager.utils.create_empty_dataset) create_empty_group() (in module pymif.microscope_manager.utils.create_empty_group) (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method)

D

data (pymif.microscope_manager.array_manager.ArrayManager attribute) (pymif.microscope_manager.ArrayManager attribute) (pymif.microscope_manager.microscope_manager.MicroscopeManager attribute)

DEFAULT_COLORS (in module pymif.microscope_manager.utils.add_label) (in module pymif.microscope_manager.utils.to_zarr) downsample_nn() (in module pymif.microscope_manager.utils.pyramid)

G

get_available_datasets() (pymif.microscope_manager.luxendo_manager.LuxendoManager method) (pymif.microscope_manager.LuxendoManager method)

L

LuxendoManager (class in pymif.microscope_manager) (class in pymif.microscope_manager.luxendo_manager)

M

metadata (pymif.microscope_manager.array_manager.ArrayManager attribute) (pymif.microscope_manager.ArrayManager attribute) (pymif.microscope_manager.microscope_manager.MicroscopeManager attribute) (pymif.microscope_manager.zarr_manager.ZarrManager attribute) (pymif.microscope_manager.ZarrManager attribute) MicroscopeManager (class in pymif.microscope_manager.microscope_manager) mode (pymif.microscope_manager.zarr_manager.ZarrManager attribute) (pymif.microscope_manager.ZarrManager attribute) module pymif pymif.microscope_manager pymif.microscope_manager.array_manager pymif.microscope_manager.luxendo_manager pymif.microscope_manager.microscope_manager pymif.microscope_manager.opera_manager pymif.microscope_manager.utils pymif.microscope_manager.utils.add_label pymif.microscope_manager.utils.create_empty_dataset pymif.microscope_manager.utils.create_empty_group pymif.microscope_manager.utils.load_label pymif.microscope_manager.utils.pyramid pymif.microscope_manager.utils.subset pymif.microscope_manager.utils.to_zarr pymif.microscope_manager.utils.visualize pymif.microscope_manager.utils.write_image_region pymif.microscope_manager.utils.write_label_region pymif.microscope_manager.viventis_manager pymif.microscope_manager.zarr_manager pymif.microscope_manager.zeiss_manager

O

OperaManager (class in pymif.microscope_manager) (class in pymif.microscope_manager.opera_manager)

P

pad_to_divisible() (in module pymif.microscope_manager.utils.pyramid) path (pymif.microscope_manager.luxendo_manager.LuxendoManager attribute) (pymif.microscope_manager.LuxendoManager attribute) (pymif.microscope_manager.opera_manager.OperaManager attribute) (pymif.microscope_manager.OperaManager attribute) (pymif.microscope_manager.viventis_manager.ViventisManager attribute) (pymif.microscope_manager.ViventisManager attribute) (pymif.microscope_manager.zarr_manager.ZarrManager attribute) (pymif.microscope_manager.ZarrManager attribute) (pymif.microscope_manager.zeiss_manager.ZeissManager attribute) (pymif.microscope_manager.ZeissManager attribute) pymif module pymif.microscope_manager module pymif.microscope_manager.array_manager module pymif.microscope_manager.luxendo_manager module pymif.microscope_manager.microscope_manager module pymif.microscope_manager.opera_manager module pymif.microscope_manager.utils module

pymif.microscope_manager.utils.add_label module pymif.microscope_manager.utils.create_empty_dataset module pymif.microscope_manager.utils.create_empty_group module pymif.microscope_manager.utils.load_label module pymif.microscope_manager.utils.pyramid module pymif.microscope_manager.utils.subset module pymif.microscope_manager.utils.to_zarr module pymif.microscope_manager.utils.visualize module pymif.microscope_manager.utils.write_image_region module pymif.microscope_manager.utils.write_label_region module pymif.microscope_manager.viventis_manager module pymif.microscope_manager.zarr_manager module pymif.microscope_manager.zeiss_manager module

R

read() (pymif.microscope_manager.array_manager.ArrayManager method) (pymif.microscope_manager.ArrayManager method) (pymif.microscope_manager.luxendo_manager.LuxendoManager method) (pymif.microscope_manager.LuxendoManager method) (pymif.microscope_manager.microscope_manager.MicroscopeManager method) (pymif.microscope_manager.opera_manager.OperaManager method) (pymif.microscope_manager.OperaManager method) (pymif.microscope_manager.viventis_manager.ViventisManager method) (pymif.microscope_manager.ViventisManager method) (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method) (pymif.microscope_manager.zeiss_manager.ZeissManager method) (pymif.microscope_manager.ZeissManager method)

reorder_channels() (pymif.microscope_manager.microscope_manager.MicroscopeManager method)

S

scenes (pymif.microscope_manager.zeiss_manager.ZeissManager attribute) (pymif.microscope_manager.ZeissManager attribute)

subset_dask_array() (in module pymif.microscope_manager.utils.subset) subset_dataset() (pymif.microscope_manager.microscope_manager.MicroscopeManager method) subset_metadata() (in module pymif.microscope_manager.utils.subset)

T

to_zarr() (in module pymif.microscope_manager.utils.to_zarr) (pymif.microscope_manager.microscope_manager.MicroscopeManager method)

U

update_metadata() (pymif.microscope_manager.microscope_manager.MicroscopeManager method)

V

validate_uniform_spacing() (in module pymif.microscope_manager.utils.subset) visualize() (in module pymif.microscope_manager.utils.visualize) (pymif.microscope_manager.microscope_manager.MicroscopeManager method)

visualize_zarr() (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method) ViventisManager (class in pymif.microscope_manager) (class in pymif.microscope_manager.viventis_manager)

W

write_image_region() (in module pymif.microscope_manager.utils.write_image_region) (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method)

write_label_region() (in module pymif.microscope_manager.utils.write_label_region) (pymif.microscope_manager.zarr_manager.ZarrManager method) (pymif.microscope_manager.ZarrManager method)

Z

ZarrManager (class in pymif.microscope_manager) (class in pymif.microscope_manager.zarr_manager)

ZeissManager (class in pymif.microscope_manager) (class in pymif.microscope_manager.zeiss_manager)