imctoolkit
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imctoolkit
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Index
Index
_
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A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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V
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W
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X
_
__init__() (ImageSingleCellData method)
(MultichannelImage method)
(SpatialCellGraph method)
A
acquisition_id (imctoolkit.MultichannelImage.read_imc_mcd parameter)
adj_mat (imctoolkit.SpatialCellGraph parameter)
aggr (imctoolkit.ImageSingleCellData.compute_cell_intensities parameter)
angle (imctoolkit.utils.rotate_centered_cv2 parameter)
AREA (ImageSingleCellData.RegionProperties attribute)
arr (imctoolkit.utils.to_table parameter)
B
BBOX (ImageSingleCellData.RegionProperties attribute)
BBOX_AREA (ImageSingleCellData.RegionProperties attribute)
border_mode (imctoolkit.utils.rotate_centered_cv2 parameter)
C
cell_centroids() (ImageSingleCellData property)
cell_channel_properties (imctoolkit.ImageSingleCellData.to_anndata parameter)
(imctoolkit.ImageSingleCellData.to_dataframe parameter)
(imctoolkit.ImageSingleCellData.to_dataset parameter)
(imctoolkit.ImageSingleCellData.write_csv parameter)
(imctoolkit.ImageSingleCellData.write_fcs parameter)
(imctoolkit.SpatialCellGraph parameter)
(imctoolkit.SpatialCellGraph.construct_dist_graph parameter)
(imctoolkit.SpatialCellGraph.construct_knn_graph parameter)
cell_ids() (ImageSingleCellData property)
(SpatialCellGraph property)
cell_properties (imctoolkit.ImageSingleCellData.to_anndata parameter)
(imctoolkit.ImageSingleCellData.to_dataframe parameter)
(imctoolkit.ImageSingleCellData.to_dataset parameter)
(imctoolkit.ImageSingleCellData.write_csv parameter)
(imctoolkit.ImageSingleCellData.write_fcs parameter)
(imctoolkit.SpatialCellGraph parameter)
(imctoolkit.SpatialCellGraph.construct_dist_graph parameter)
(imctoolkit.SpatialCellGraph.construct_knn_graph parameter)
channel_names (imctoolkit.ImageSingleCellData parameter)
(imctoolkit.MultichannelImage parameter)
(imctoolkit.MultichannelImage.read_tiff parameter)
channel_names() (ImageSingleCellData property)
(MultichannelImage property)
channel_names_attr (imctoolkit.MultichannelImage.read_imc_mcd parameter)
(imctoolkit.MultichannelImage.read_imc_txt parameter)
compute_cell_border_distances() (ImageSingleCellData method)
compute_cell_centroid_distances() (ImageSingleCellData method)
compute_cell_intensities() (ImageSingleCellData method)
construct_dist_graph() (SpatialCellGraph class method)
construct_knn_graph() (SpatialCellGraph class method)
CONVEX_AREA (ImageSingleCellData.RegionProperties attribute)
CONVEX_IMAGE (ImageSingleCellData.RegionProperties attribute)
COORDS (ImageSingleCellData.RegionProperties attribute)
copy() (MultichannelImage method)
create_using (imctoolkit.SpatialCellGraph.to_networkx parameter)
D
data (imctoolkit.MultichannelImage parameter)
(imctoolkit.SpatialCellGraph parameter)
(imctoolkit.SpatialCellGraph.construct_dist_graph parameter)
(imctoolkit.SpatialCellGraph.construct_knn_graph parameter)
dataset (imctoolkit.SpatialCellGraph.load_dataset parameter)
DEFAULT_REGION_PROPERTIES (ImageSingleCellData attribute)
dist_mat (imctoolkit.SpatialCellGraph.construct_dist_graph parameter)
(imctoolkit.SpatialCellGraph.construct_knn_graph parameter)
dist_thres (imctoolkit.SpatialCellGraph.construct_dist_graph parameter)
E
ECCENTRICITY (ImageSingleCellData.RegionProperties attribute)
EQUIVALENT_DIAMETER (ImageSingleCellData.RegionProperties attribute)
EULER_NUMBER (ImageSingleCellData.RegionProperties attribute)
expand_bbox (imctoolkit.utils.rotate_centered_cv2 parameter)
EXTENT (ImageSingleCellData.RegionProperties attribute)
F
feature_names() (SpatialCellGraph property)
FILLED_AREA (ImageSingleCellData.RegionProperties attribute)
FILLED_IMAGE (ImageSingleCellData.RegionProperties attribute)
G
gaussian_filter_cv2() (in module imctoolkit.utils)
H
height() (MultichannelImage property)
hot_pixel_filter() (in module imctoolkit.utils)
hot_pixel_thres (imctoolkit.utils.hot_pixel_filter parameter)
I
IMAGE (ImageSingleCellData.RegionProperties attribute)
image_height() (ImageSingleCellData property)
image_width() (ImageSingleCellData property)
ImageSingleCellData (class in imctoolkit)
ImageSingleCellData.RegionProperties (class in imctoolkit)
imctoolkit.utils
module
img (imctoolkit.ImageSingleCellData parameter)
(imctoolkit.utils.gaussian_filter_cv2 parameter)
(imctoolkit.utils.hot_pixel_filter parameter)
(imctoolkit.utils.median_filter_cv2 parameter)
(imctoolkit.utils.rotate_centered_cv2 parameter)
INERTIA_TENSOR (ImageSingleCellData.RegionProperties attribute)
INERTIA_TENSOR_EIGVALS (ImageSingleCellData.RegionProperties attribute)
inplace (imctoolkit.utils.gaussian_filter_cv2 parameter)
(imctoolkit.utils.hot_pixel_filter parameter)
(imctoolkit.utils.median_filter_cv2 parameter)
(imctoolkit.utils.rotate_centered_cv2 parameter)
is_undirected() (SpatialCellGraph property)
K
k (imctoolkit.SpatialCellGraph.construct_knn_graph parameter)
kwargs (imctoolkit.ImageSingleCellData.write_csv parameter)
(imctoolkit.ImageSingleCellData.write_fcs parameter)
(imctoolkit.MultichannelImage.read parameter)
(imctoolkit.MultichannelImage.write_ome_tiff parameter)
L
load_dataset() (SpatialCellGraph static method)
LOCAL_CENTROID (ImageSingleCellData.RegionProperties attribute)
M
MAJOR_AXIS_LENGTH (ImageSingleCellData.RegionProperties attribute)
mask (imctoolkit.ImageSingleCellData parameter)
max_intensities() (ImageSingleCellData property)
max_intensities_table() (ImageSingleCellData property)
mean_intensities() (ImageSingleCellData property)
mean_intensities_table() (ImageSingleCellData property)
median_filter_cv2() (in module imctoolkit.utils)
median_intensities() (ImageSingleCellData property)
median_intensities_table() (ImageSingleCellData property)
metric (imctoolkit.ImageSingleCellData.compute_cell_centroid_distances parameter)
min_intensities() (ImageSingleCellData property)
min_intensities_table() (ImageSingleCellData property)
MINOR_AXIS_LENGTH (ImageSingleCellData.RegionProperties attribute)
mode (imctoolkit.SpatialCellGraph.to_igraph parameter)
module
imctoolkit.utils
MOMENTS (ImageSingleCellData.RegionProperties attribute)
MOMENTS_CENTRAL (ImageSingleCellData.RegionProperties attribute)
MOMENTS_HU (ImageSingleCellData.RegionProperties attribute)
MOMENTS_NORMALIZED (ImageSingleCellData.RegionProperties attribute)
MultichannelImage (class in imctoolkit)
N
num_cells() (ImageSingleCellData property)
(SpatialCellGraph property)
num_channels() (ImageSingleCellData property)
(MultichannelImage property)
num_features() (SpatialCellGraph property)
O
ome_channel_name_attr (imctoolkit.MultichannelImage.read_tiff parameter)
ORIENTATION (ImageSingleCellData.RegionProperties attribute)
P
panel (imctoolkit.MultichannelImage.read_tiff parameter)
panel_channel_index_col (imctoolkit.MultichannelImage.read_tiff parameter)
panel_channel_name_col (imctoolkit.MultichannelImage.read_tiff parameter)
path (imctoolkit.ImageSingleCellData.write_csv parameter)
(imctoolkit.ImageSingleCellData.write_fcs parameter)
(imctoolkit.MultichannelImage.read parameter)
(imctoolkit.MultichannelImage.read_imc_mcd parameter)
(imctoolkit.MultichannelImage.read_imc_txt parameter)
(imctoolkit.MultichannelImage.read_tiff parameter)
(imctoolkit.MultichannelImage.write_ome_tiff parameter)
PERIMETER (ImageSingleCellData.RegionProperties attribute)
R
read() (MultichannelImage class method)
read_imc_mcd() (MultichannelImage static method)
read_imc_txt() (MultichannelImage static method)
read_tiff() (MultichannelImage static method)
region_properties (imctoolkit.ImageSingleCellData parameter)
regionprops() (ImageSingleCellData property)
regionprops_table() (ImageSingleCellData property)
rotate_centered_cv2() (in module imctoolkit.utils)
S
sigma (imctoolkit.utils.gaussian_filter_cv2 parameter)
size (imctoolkit.utils.gaussian_filter_cv2 parameter)
(imctoolkit.utils.median_filter_cv2 parameter)
SLICE (ImageSingleCellData.RegionProperties attribute)
SOLIDITY (ImageSingleCellData.RegionProperties attribute)
SpatialCellGraph (class in imctoolkit)
std_intensities() (ImageSingleCellData property)
std_intensities_table() (ImageSingleCellData property)
T
to_anndata() (ImageSingleCellData method)
to_dataframe() (ImageSingleCellData method)
to_dataset() (ImageSingleCellData method)
(SpatialCellGraph method)
to_igraph() (SpatialCellGraph method)
to_networkx() (SpatialCellGraph method)
to_table() (in module imctoolkit.utils)
V
var_intensities() (ImageSingleCellData property)
var_intensities_table() (ImageSingleCellData property)
W
weight_mat (imctoolkit.SpatialCellGraph.to_networkx parameter)
width() (MultichannelImage property)
write_csv() (ImageSingleCellData method)
write_fcs() (ImageSingleCellData method)
write_ome_tiff() (MultichannelImage method)
X
x_cell_channel_property (imctoolkit.ImageSingleCellData.to_anndata parameter)