Index

A

add_objects() (in module qubalab.qupath.qupath_gateway) add_plane_to_geometry() (in module qubalab.objects.geometry)

ANNOTATION (qubalab.objects.object_type.ObjectType attribute) as_tuple() (qubalab.images.metadata.image_shape.ImageShape method)

B

base64_to_image() (in module qubalab.images.utils)

base_server (qubalab.images.wrapped_image_server.WrappedImageServer property) bytes_to_image() (in module qubalab.images.utils)

C

c (qubalab.images.metadata.image_shape.ImageShape attribute) CELL (qubalab.objects.object_type.ObjectType attribute) channels (qubalab.images.metadata.image_metadata.ImageMetadata property) Classification (class in qubalab.objects.classification) classification (qubalab.objects.image_feature.ImageFeature property) close() (qubalab.images.image_server.ImageServer method) (qubalab.images.labeled_server.LabeledImageServer method) (qubalab.images.openslide_server.OpenSlideServer method) (qubalab.images.qupath_server.QuPathServer method) (qubalab.images.wrapped_image_server.WrappedImageServer method)

color (qubalab.images.metadata.image_channel.ImageChannel attribute) (qubalab.objects.classification.Classification property) (qubalab.objects.image_feature.ImageFeature property) count_objects() (in module qubalab.qupath.qupath_gateway) create_from_feature() (qubalab.objects.image_feature.ImageFeature class method) create_from_label_image() (qubalab.objects.image_feature.ImageFeature class method) create_gateway() (in module qubalab.qupath.qupath_gateway) create_microns() (qubalab.images.metadata.pixel_calibration.PixelLength static method) create_snapshot() (in module qubalab.qupath.qupath_gateway) create_unknown() (qubalab.images.metadata.pixel_calibration.PixelLength static method)

D

delete_objects() (in module qubalab.qupath.qupath_gateway) DETECTION (qubalab.objects.object_type.ObjectType attribute)

downsample_region() (qubalab.images.region_2d.Region2D method) downsamples (qubalab.images.metadata.image_metadata.ImageMetadata property) draw_geometry() (in module qubalab.objects.draw)

F

from_tczyx() (qubalab.images.metadata.image_shape.ImageShape method)

G

geojson_features_from_string() (in module qubalab.objects.geojson) geometry (qubalab.images.region_2d.Region2D property) get_cached_classification() (qubalab.objects.classification.Classification static method)

get_current_image_data() (in module qubalab.qupath.qupath_gateway) get_default_gateway() (in module qubalab.qupath.qupath_gateway) get_objects() (in module qubalab.qupath.qupath_gateway) get_project() (in module qubalab.qupath.qupath_gateway)

H

height (qubalab.images.metadata.image_metadata.ImageMetadata property) (qubalab.images.region_2d.Region2D attribute)

I

icc_transform (qubalab.images.icc_profile_server.IccProfileServer property) IccProfileServer (class in qubalab.images.icc_profile_server) ImageChannel (class in qubalab.images.metadata.image_channel) ImageFeature (class in qubalab.objects.image_feature) ImageMetadata (class in qubalab.images.metadata.image_metadata) ImagePlane (class in qubalab.objects.geometry) ImageServer (class in qubalab.images.image_server)

ImageShape (class in qubalab.images.metadata.image_shape) is_annotation (qubalab.objects.image_feature.ImageFeature property) is_calibrated() (qubalab.images.metadata.pixel_calibration.PixelCalibration method) is_cell (qubalab.objects.image_feature.ImageFeature property) is_default() (qubalab.images.metadata.pixel_calibration.PixelLength method) is_detection (qubalab.objects.image_feature.ImageFeature property) is_tile (qubalab.objects.image_feature.ImageFeature property)

L

LabeledImageServer (class in qubalab.images.labeled_server) length (qubalab.images.metadata.pixel_calibration.PixelLength attribute) length_x (qubalab.images.metadata.pixel_calibration.PixelCalibration attribute)

length_y (qubalab.images.metadata.pixel_calibration.PixelCalibration attribute) length_z (qubalab.images.metadata.pixel_calibration.PixelCalibration attribute) level_to_dask() (qubalab.images.image_server.ImageServer method)

M

measurements (qubalab.objects.image_feature.ImageFeature property) metadata (qubalab.images.image_server.ImageServer property) module qubalab.display.plot qubalab.images.icc_profile_server qubalab.images.image_server qubalab.images.labeled_server qubalab.images.metadata.image_channel qubalab.images.metadata.image_metadata qubalab.images.metadata.image_shape qubalab.images.metadata.pixel_calibration qubalab.images.openslide_server qubalab.images.qupath_server qubalab.images.region_2d qubalab.images.utils qubalab.images.wrapped_image_server qubalab.objects.classification qubalab.objects.draw qubalab.objects.geojson qubalab.objects.geometry qubalab.objects.image_feature qubalab.objects.object_type qubalab.qupath.qupath_gateway

N

n_channels (qubalab.images.metadata.image_metadata.ImageMetadata property) n_resolutions (qubalab.images.metadata.image_metadata.ImageMetadata property) n_timepoints (qubalab.images.metadata.image_metadata.ImageMetadata property) n_z_slices (qubalab.images.metadata.image_metadata.ImageMetadata property)

name (qubalab.images.metadata.image_channel.ImageChannel attribute) (qubalab.objects.classification.Classification property) (qubalab.objects.image_feature.ImageFeature property) nucleus_geometry (qubalab.objects.image_feature.ImageFeature property)

O

object_type (qubalab.objects.image_feature.ImageFeature property)

ObjectType (class in qubalab.objects.object_type) OpenSlideServer (class in qubalab.images.openslide_server)

P

PixelCalibration (class in qubalab.images.metadata.pixel_calibration) PixelLength (class in qubalab.images.metadata.pixel_calibration)

plotImage() (in module qubalab.display.plot) plotImageFeatures() (in module qubalab.display.plot)

Q

qubalab.display.plot module qubalab.images.icc_profile_server module qubalab.images.image_server module qubalab.images.labeled_server module qubalab.images.metadata.image_channel module qubalab.images.metadata.image_metadata module qubalab.images.metadata.image_shape module qubalab.images.metadata.pixel_calibration module qubalab.images.openslide_server module qubalab.images.qupath_server module

qubalab.images.region_2d module qubalab.images.utils module qubalab.images.wrapped_image_server module qubalab.objects.classification module qubalab.objects.draw module qubalab.objects.geojson module qubalab.objects.geometry module qubalab.objects.image_feature module qubalab.objects.object_type module qubalab.qupath.qupath_gateway module QuPathServer (class in qubalab.images.qupath_server)

R

read_region() (qubalab.images.image_server.ImageServer method) refresh_qupath() (in module qubalab.qupath.qupath_gateway)

Region2D (class in qubalab.images.region_2d) ROOT (qubalab.objects.object_type.ObjectType attribute)

S

scale_region() (qubalab.images.region_2d.Region2D method)

set_default_gateway() (in module qubalab.qupath.qupath_gateway) shape (qubalab.images.metadata.image_metadata.ImageMetadata property)

T

t (qubalab.images.metadata.image_shape.ImageShape attribute) (qubalab.images.region_2d.Region2D attribute)

TILE (qubalab.objects.object_type.ObjectType attribute) TMA_CORE (qubalab.objects.object_type.ObjectType attribute) to_dask() (qubalab.images.image_server.ImageServer method)

U

unit (qubalab.images.metadata.pixel_calibration.PixelLength attribute)

W

width (qubalab.images.metadata.image_metadata.ImageMetadata property) (qubalab.images.region_2d.Region2D attribute)

WrappedImageServer (class in qubalab.images.wrapped_image_server)

X

x (qubalab.images.metadata.image_shape.ImageShape attribute) (qubalab.images.region_2d.Region2D attribute)

Y

y (qubalab.images.metadata.image_shape.ImageShape attribute) (qubalab.images.region_2d.Region2D attribute)

Z

z (qubalab.images.metadata.image_shape.ImageShape attribute) (qubalab.images.region_2d.Region2D attribute)