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) _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)

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)

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.write) 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) MicroscopeManager (class in pymif.microscope_manager.microscope_manager) 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.pyramid pymif.microscope_manager.utils.subset pymif.microscope_manager.utils.visualize pymif.microscope_manager.utils.write 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.pyramid module pymif.microscope_manager.utils.subset module pymif.microscope_manager.utils.visualize module pymif.microscope_manager.utils.write 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

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)

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() (in module pymif.microscope_manager.utils.write) (pymif.microscope_manager.microscope_manager.MicroscopeManager 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)