campa
stable
Contents
Installation
Overview
API
Classes
CLI
Tutorials
campa
Index
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Index
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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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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U
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V
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W
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X
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Y
A
add_cluster_annotation() (Cluster method)
add_cluster_colors() (Cluster method)
add_clustering_to_adata() (in module campa.tl)
add_conditions() (MPPData method)
add_data_config() (CAMPAConfig method)
add_data_from_dir() (MPPData method)
add_neighborhood() (MPPData method)
add_noise() (BaseAEModel method)
(VAEModel method)
add_umap() (Cluster method)
annotate_img() (in module campa.pl)
apply_mask() (MPPData method)
B
BASE_DATA_DIR (CAMPAConfig property)
BaseAEModel (class in campa.tl)
C
campa
module
campa.data
module
campa.pl
module
campa.tl
module
campa_config (in module campa.constants)
CAMPAConfig (class in campa.constants)
center_mpp (MPPData property)
channels (MPPData attribute)
Cluster (class in campa.tl)
cluster_annotation (Cluster property)
cluster_mpp (Cluster property)
CO_OCC_CHUNK_SIZE (CAMPAConfig property)
concat() (MPPData class method)
conditions (MPPData property)
config (Cluster attribute)
(Experiment attribute)
config_fname (CAMPAConfig property)
copy() (MPPData method)
create_adversarial_head() (BaseAEModel method)
(VAEModel method)
create_cluster_data() (in module campa.tl)
create_cluster_mpp() (Cluster method)
create_clustering() (Cluster method)
create_dataset() (in module campa.data)
create_decoder() (BaseAEModel method)
(VAEModel method)
create_encoder() (BaseAEModel method)
(VAEModel method)
create_model() (BaseAEModel method)
(Estimator method)
(VAEModel method)
D
data (NNDataset attribute)
data() (MPPData method)
data_configs (CAMPAConfig property)
default_config (BaseAEModel attribute)
(VAEModel attribute)
dir (Experiment property)
E
encode_condition() (BaseAEModel method)
(VAEModel method)
epoch (Experiment property)
Estimator (class in campa.tl)
estimator_config (Experiment property)
evaluate_config (Experiment property)
evaluate_model() (Estimator method)
(Predictor method)
Experiment (class in campa.tl)
EXPERIMENT_DIR (CAMPAConfig property)
extract_co_occurrence() (FeatureExtractor method)
extract_co_occurrence_csv() (FeatureExtractor method)
extract_csv() (MPPData method)
extract_features() (in module campa.tl)
extract_intensity_csv() (FeatureExtractor method)
extract_intensity_size() (FeatureExtractor method)
extract_object_stats() (FeatureExtractor method)
extract_object_stats_csv() (FeatureExtractor method)
F
FeatureExtractor (class in campa.tl)
from_adata() (FeatureExtractor class method)
from_cluster_data_dir() (Cluster class method)
from_data_dir() (MPPData class method)
from_dir() (Experiment class method)
(ModelComparator class method)
from_exp() (Cluster class method)
from_exp_split() (Cluster class method)
full_path (Experiment property)
G
get_adata() (MPPData method)
get_channel_ids() (MPPData method)
get_cluster_annotation() (Experiment method)
get_clustered_cells() (in module campa.tl)
get_condition() (MPPData method)
get_data_config() (CAMPAConfig method)
get_experiments_from_config() (Experiment static method)
get_experiments_from_dir() (Experiment static method)
get_history() (Experiment method)
get_hpa_localisation() (Cluster method)
get_img() (MPPData method)
get_intensity_adata() (FeatureExtractor method)
get_intensity_change() (in module campa.pl)
get_nndescent_index() (Cluster method)
get_object_img() (MPPData method)
get_object_imgs() (MPPData method)
get_object_stats() (FeatureExtractor method)
get_representation() (Predictor method)
get_split_cluster_annotation() (Experiment method)
get_split_imgs_mpp_data() (Experiment method)
get_split_mpp_data() (Experiment method)
get_tf_dataset() (NNDataset method)
H
has_neighbor_data (MPPData property)
I
imgs (NNDataset attribute)
init_logging() (in module campa.utils)
is_adversarial (BaseAEModel property)
(VAEModel property)
is_conditional (BaseAEModel property)
(VAEModel property)
is_trainable (Experiment property)
L
latent (MPPData property)
load_config() (in module campa.utils)
load_example_data() (in module campa.data)
load_example_experiment() (in module campa.data)
load_full_data_dict() (in module campa.tl)
LossEnum (class in campa.tl)
M
merged_config() (in module campa.utils)
metadata (MPPData attribute)
ModelComparator (class in campa.tl)
ModelEnum (class in campa.tl)
module
campa
campa.data
campa.pl
campa.tl
mpp (MPPData property)
mpp_data (FeatureExtractor property)
MPPData (class in campa.data)
N
name (Experiment property)
NNDataset (class in campa.data)
normalise() (MPPData method)
O
obj_ids (MPPData property)
P
plot_cluster_images() (ModelComparator method)
plot_co_occurrence() (in module campa.pl)
plot_co_occurrence_grid() (in module campa.pl)
plot_final_score() (ModelComparator method)
plot_history() (ModelComparator method)
plot_intensity_change() (in module campa.pl)
plot_mean_intensity() (in module campa.pl)
plot_mean_size() (in module campa.pl)
plot_object_stats() (in module campa.pl)
plot_per_channel_mse() (ModelComparator method)
plot_predicted_images() (ModelComparator method)
plot_size_change() (in module campa.pl)
plot_umap() (ModelComparator method)
predict() (Predictor method)
predict_cluster_imgs() (Cluster method)
predict_cluster_rep() (Cluster method)
predict_model() (Estimator method)
predict_split() (Predictor method)
Predictor (class in campa.tl)
prepare() (MPPData method)
prepare_full_dataset() (in module campa.tl)
project_cluster_data() (in module campa.tl)
project_clustering() (Cluster method)
R
run_experiments() (in module campa.tl)
S
save_dir (ModelComparator attribute)
set_cluster_name() (Cluster method)
set_to_evaluate() (Experiment method)
subsample() (MPPData method)
subset() (MPPData method)
subset_channels() (MPPData method)
T
test_dataset (Estimator property)
thresholded_count() (in module campa.tl)
thresholded_median() (in module campa.tl)
train_dataset (Estimator property)
train_model() (Estimator method)
train_val_test_split() (MPPData method)
U
unique_obj_ids (MPPData property)
V
VAEModel (class in campa.tl)
val_dataset (Estimator property)
W
write() (CAMPAConfig method)
(MPPData method)
X
x (MPPData property)
x() (NNDataset method)
Y
y (MPPData property)
y() (NNDataset method)
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