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One-class segmentation with 2D U-Net
Cascaded architecture
Estimate uncertainty
Optimize Hyperparameters
Two-class microscopy segmentation with 2D U-Net
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ivadomed
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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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O
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P
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V
_
__call__() (AdditiveGaussianNoise method)
(BoundingBoxCrop method)
(CenterCrop method)
(Clahe method)
(Compose method)
(Crop method)
(DilateGT method)
(ElasticTransform method)
(HistogramClipping method)
(ImedTransform method)
(MetricManager method)
(NormalizeInstance method)
(NumpyToTensor method)
(RandomAffine method)
(RandomBiasField method)
(RandomBlur method)
(RandomGamma method)
(RandomReverse method)
(RandomShiftIntensity method)
(Resample method)
(ROICrop method)
(UndoCompose method)
(UndoTransform method)
__getitem__() (CroppableArray method)
__init__() (AdapWingLoss method)
(AdditiveGaussianNoise method)
(AnimatedGif method)
(BinaryCrossEntropyLoss method)
(Clahe method)
(Compose method)
(Countception method)
(Crop method)
(DenseNet method)
(DiceLoss method)
(DilateGT method)
(ElasticTransform method)
(Evaluation3DMetrics method)
(FiLMedUnet method)
(FocalDiceLoss method)
(FocalLoss method)
(FocalTverskyLoss method)
(GeneralizedDiceLoss method)
(HeMISUnet method)
(HistogramClipping method)
(HookBasedFeatureExtractor method)
(Kde_model method)
(L2loss method)
(LossCombination method)
(MetricManager method)
(Modified3DUNet method)
(MultiClassDiceLoss method)
(Postprocessing method)
(RandomAffine method)
(RandomBiasField method)
(RandomBlur method)
(RandomGamma method)
(RandomShiftIntensity method)
(Resample method)
(ResNet method)
(TverskyLoss method)
(UndoCompose method)
(UndoTransform method)
(Unet method)
A
accuracy_score() (in module ivadomed.metrics)
AdapWingLoss (class in ivadomed.losses)
AdditiveGaussianNoise (class in ivadomed.transforms)
adjust_bb_size() (in module ivadomed.object_detection.utils)
adjust_transforms() (in module ivadomed.object_detection.utils)
adjust_undo_transforms() (in module ivadomed.object_detection.utils)
AnimatedGif (class in ivadomed.visualize)
apply() (Postprocessing method)
apply_preprocessing_transforms() (in module ivadomed.transforms)
ArgParseException
automate_training() (in module ivadomed.scripts.automate_training)
B
binarize_maxpooling() (Postprocessing method)
binarize_prediction() (Postprocessing method)
binarize_with_low_threshold() (in module ivadomed.postprocessing)
BinaryCrossEntropyLoss (class in ivadomed.losses)
bounding_box_prior() (in module ivadomed.object_detection.utils)
BoundingBoxCrop (class in ivadomed.transforms)
C
CenterCrop (class in ivadomed.transforms)
check_exe() (in module ivadomed.utils)
check_isMRIparam() (in module ivadomed.loader.film)
Clahe (class in ivadomed.transforms)
clustering_fit() (in module ivadomed.loader.film)
combine_predictions() (in module ivadomed.uncertainty)
Compose (class in ivadomed.transforms)
compute_bb_statistics() (in module ivadomed.object_detection.utils)
compute_statistics() (in module ivadomed.scripts.compare_models)
convert_labels_to_RGB() (in module ivadomed.visualize)
convert_pytorch_to_onnx() (in module ivadomed.scripts.convert_to_onnx)
coordinate_from_heatmap() (in module ivadomed.postprocessing)
Countception (class in ivadomed.models)
create_temp_directory() (in module ivadomed.loader.utils)
Crop (class in ivadomed.transforms)
CroppableArray (class in ivadomed.transforms)
cuda() (in module ivadomed.utils)
D
define_device() (in module ivadomed.utils)
DenseNet (class in ivadomed.models)
dice_score() (in module ivadomed.metrics)
DiceLoss (class in ivadomed.losses)
DilateGT (class in ivadomed.transforms)
display_selected_model_spec() (in module ivadomed.utils)
display_selected_transfoms() (in module ivadomed.utils)
dropout_input() (in module ivadomed.loader.utils)
E
ElasticTransform (class in ivadomed.transforms)
evaluate() (in module ivadomed.evaluation)
Evaluation3DMetrics (class in ivadomed.evaluation)
extract_mid_slice_and_convert_coordinates_to_heatmaps() (in module ivadomed.scripts.prepare_dataset_vertebral_labeling)
extract_small_dataset() (in module ivadomed.scripts.extract_small_dataset)
F
fill_holes() (in module ivadomed.postprocessing)
(Postprocessing method)
FiLMedUnet (class in ivadomed.models)
filter_roi() (in module ivadomed.loader.utils)
finish() (LoopingPillowWriter method)
FocalDiceLoss (class in ivadomed.losses)
FocalLoss (class in ivadomed.losses)
FocalTverskyLoss (class in ivadomed.losses)
format_path_data() (in module ivadomed.utils)
forward() (AdapWingLoss method)
(BinaryCrossEntropyLoss method)
(Countception method)
(DenseNet method)
(DiceLoss method)
(FiLMedUnet method)
(FocalDiceLoss method)
(FocalLoss method)
(FocalTverskyLoss method)
(GeneralizedDiceLoss method)
(HeMISUnet method)
(HookBasedFeatureExtractor method)
(L2loss method)
(LossCombination method)
(Modified3DUNet method)
(MultiClassDiceLoss method)
(ResNet method)
(TverskyLoss method)
(Unet method)
G
gaussian_kernel() (in module ivadomed.maths)
GeneralizedDiceLoss (class in ivadomed.losses)
generate_bounding_box_file() (in module ivadomed.object_detection.utils)
generate_sha_256() (in module ivadomed.utils)
get_arguments() (in module ivadomed.utils)
get_avd() (Evaluation3DMetrics method)
get_bounding_boxes() (in module ivadomed.object_detection.utils)
get_file_extension() (in module ivadomed.loader.utils)
get_film_metadata_models() (in module ivadomed.loader.film)
get_gt() (in module ivadomed.testing)
get_lfdr() (Evaluation3DMetrics method)
get_linux_system_memory() (in module ivadomed.utils)
get_loss_function() (in module ivadomed.training)
get_ltpr() (Evaluation3DMetrics method)
get_mac_system_memory() (in module ivadomed.utils)
get_metadata() (in module ivadomed.training)
get_new_subject_file_split() (in module ivadomed.loader.utils)
get_obj_size() (in module ivadomed.loader.utils)
get_onehotencoder() (in module ivadomed.inference)
get_param_list() (in module ivadomed.scripts.automate_training)
get_preds() (in module ivadomed.inference)
get_preprocessing_transforms() (in module ivadomed.transforms)
get_rvd() (Evaluation3DMetrics method)
get_sampler() (in module ivadomed.training)
get_scheduler() (in module ivadomed.training)
get_subdatasets_subject_files_list() (in module ivadomed.loader.utils)
get_subdatasets_transforms() (in module ivadomed.transforms)
get_system_memory() (in module ivadomed.utils)
get_timestamp() (in module ivadomed.utils)
get_vol() (Evaluation3DMetrics method)
get_win_system_memory() (in module ivadomed.utils)
H
hausdorff_score() (in module ivadomed.metrics)
heatmap_generation() (in module ivadomed.maths)
HeMISUnet (class in ivadomed.models)
HistogramClipping (class in ivadomed.transforms)
HookBasedFeatureExtractor (class in ivadomed.visualize)
HyperparameterOption() (in module ivadomed.scripts.automate_training)
I
image_reconstruction() (in module ivadomed.inference)
imed_collate() (in module ivadomed.loader.utils)
ImedTransform (class in ivadomed.transforms)
init_ivadomed() (in module ivadomed.utils)
initialize_wandb() (in module ivadomed.utils)
install_data() (in module ivadomed.scripts.download_data)
intersection_over_union() (in module ivadomed.metrics)
ivadomed.evaluation
module
ivadomed.inference
module
ivadomed.loader.film
module
ivadomed.loader.loader
module
ivadomed.loader.utils
module
ivadomed.losses
module
ivadomed.main
module
ivadomed.maths
module
ivadomed.metrics
module
ivadomed.mixup
module
ivadomed.object_detection.utils
module
ivadomed.postprocessing
module
ivadomed.testing
module
ivadomed.training
module
ivadomed.transforms
module
ivadomed.uncertainty
module
ivadomed.utils
module
ivadomed.visualize
module
K
Kde_model (class in ivadomed.loader.film)
keep_largest() (Postprocessing method)
keep_largest_object() (in module ivadomed.postprocessing)
keep_largest_object_per_slice() (in module ivadomed.postprocessing)
L
L2loss (class in ivadomed.losses)
label_file_from_coordinates() (in module ivadomed.postprocessing)
label_per_size() (Evaluation3DMetrics method)
load_bounding_boxes() (in module ivadomed.object_detection.utils)
load_checkpoint() (in module ivadomed.training)
load_dataset() (in module ivadomed.loader.loader)
LoopingPillowWriter (class in ivadomed.visualize)
LossCombination (class in ivadomed.losses)
M
make_config_list() (in module ivadomed.scripts.automate_training)
mask_predictions() (in module ivadomed.postprocessing)
Metavar (class in ivadomed.utils)
MetricManager (class in ivadomed.metrics)
mixup() (in module ivadomed.mixup)
Modified3DUNet (class in ivadomed.models)
module
ivadomed.evaluation
ivadomed.inference
ivadomed.loader.film
ivadomed.loader.loader
ivadomed.loader.utils
ivadomed.losses
ivadomed.main
ivadomed.maths
ivadomed.metrics
ivadomed.mixup
ivadomed.object_detection.utils
ivadomed.postprocessing
ivadomed.testing
ivadomed.training
ivadomed.transforms
ivadomed.uncertainty
ivadomed.utils
ivadomed.visualize
mse() (in module ivadomed.metrics)
multi_class_dice_score() (in module ivadomed.metrics)
multichannel_capable() (in module ivadomed.transforms)
MultiClassDiceLoss (class in ivadomed.losses)
multilabel_capable() (in module ivadomed.postprocessing)
N
nifti_capable() (in module ivadomed.postprocessing)
normalize_metadata() (in module ivadomed.loader.film)
NormalizeInstance (class in ivadomed.transforms)
numeric_score() (in module ivadomed.metrics)
NumpyToTensor (class in ivadomed.transforms)
O
onnx_inference() (in module ivadomed.inference)
orient_img_hwd() (in module ivadomed.loader.utils)
orient_img_ras() (in module ivadomed.loader.utils)
orient_shapes_hwd() (in module ivadomed.loader.utils)
overlap_im_seg() (in module ivadomed.visualize)
P
plot_dice_thr() (in module ivadomed.metrics)
plot_roc_curve() (in module ivadomed.metrics)
plot_transformed_sample() (in module ivadomed.utils)
Postprocessing (class in ivadomed.postprocessing)
precision_score() (in module ivadomed.metrics)
pred_to_nib() (in module ivadomed.inference)
pred_to_png() (in module ivadomed.inference)
prepare_transforms() (in module ivadomed.transforms)
process_transformations() (in module ivadomed.inference)
R
RandomAffine (class in ivadomed.transforms)
RandomBiasField (class in ivadomed.transforms)
RandomBlur (class in ivadomed.transforms)
RandomGamma (class in ivadomed.transforms)
RandomReverse (class in ivadomed.transforms)
RandomShiftIntensity (class in ivadomed.transforms)
recall_score() (in module ivadomed.metrics)
reconstruct_3d_object() (in module ivadomed.inference)
remove_noise() (Postprocessing method)
remove_small() (Postprocessing method)
remove_small_objects() (in module ivadomed.postprocessing)
reorient_image() (in module ivadomed.loader.utils)
Resample (class in ivadomed.transforms)
resample_bounding_box() (in module ivadomed.object_detection.utils)
rescale_values_array() (in module ivadomed.maths)
resize_to_multiple() (in module ivadomed.object_detection.utils)
ResNet (class in ivadomed.models)
ROICrop (class in ivadomed.transforms)
run_command() (in module ivadomed.main)
run_eval() (Evaluation3DMetrics method)
run_inference() (in module ivadomed.testing)
run_plot_training_curves() (in module ivadomed.scripts.training_curve)
run_uncertainty() (in module ivadomed.uncertainty)
run_visualization() (in module ivadomed.scripts.visualize_transforms)
S
save_color_labels() (in module ivadomed.visualize)
save_feature_map() (in module ivadomed.visualize)
save_film_params() (in module ivadomed.loader.film)
save_img() (in module ivadomed.visualize)
save_mixup_sample() (in module ivadomed.mixup)
save_onnx_model() (in module ivadomed.utils)
segment_image() (in module ivadomed.scripts.segment_image)
segment_volume() (in module ivadomed.inference)
set_option() (in module ivadomed.inference)
set_postprocessing_options() (in module ivadomed.inference)
similarity_score() (in module ivadomed.utils)
specificity_score() (in module ivadomed.metrics)
split_classes() (in module ivadomed.inference)
split_dataset() (in module ivadomed.loader.utils)
store_film_params() (in module ivadomed.loader.film)
structurewise_uncertainty() (in module ivadomed.uncertainty)
T
test() (in module ivadomed.testing)
threshold_analysis() (in module ivadomed.testing)
threshold_predictions() (in module ivadomed.postprocessing)
tio_transform() (in module ivadomed.transforms)
train() (in module ivadomed.training)
tversky_index() (TverskyLoss method)
TverskyLoss (class in ivadomed.losses)
two_dim_compatible() (in module ivadomed.transforms)
U
uncertainty() (Postprocessing method)
undo_transform() (NumpyToTensor method)
(Resample method)
UndoCompose (class in ivadomed.transforms)
UndoTransform (class in ivadomed.transforms)
Unet (class in ivadomed.models)
unstack_tensors() (in module ivadomed.utils)
update_dict() (in module ivadomed.scripts.automate_training)
update_filename_to_nifti() (in module ivadomed.loader.utils)
update_metadata() (in module ivadomed.loader.utils)
V
verify_metadata() (in module ivadomed.object_detection.utils)
visualize_and_compare_models() (in module ivadomed.scripts.visualize_and_compare_testing_models)
volume_reconstruction() (in module ivadomed.inference)
voxelwise_uncertainty() (in module ivadomed.uncertainty)
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