Circle of Willis-Guided Localization for Simultaneous Detection and Classification of Large Vessel Occlusions in Brain CTA.
The 2 matches
- [1] § Methods › Network Architecture ↔ nndet/arch/heads/classifier.py, lines 295–364 · score 0.68 · cross entropy loss, classification head, bounding box, convolutional, sigmoid, layer
- [2] § Methods › Network Architecture ↔ nndet/arch/decoder/base.py, lines 29–104 · score 0.66 · lateral connections, transposed convolutional, decoder, activation, layer, union
Paper
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The authors' code
Python · 430 lines · 15 KB · no license · 1 match
- """
- Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Licensed under the Apache License, Version 2.0 (the "License");
- you may not use this file except in compliance with the License.
- You may obtain a copy of the License at
- http://www.apache.org/licenses/LICENSE-2.0
- Unless required by applicable law or agreed to in writing, software
- distributed under the License is distributed on an "AS IS" BASIS,
- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- See the License for the specific language governing permissions and
- limitations under the License.
- """
- import torch
- import math
- import torch.nn as nn
- from typing import Optional, TypeVar
- from torch import Tensor
- from abc import abstractmethod
- from loguru import logger
- from nndet.losses.classification import (
- FocalLossWithLogits,
- BCEWithLogitsLossOneHot,
- CrossEntropyLoss,
- )
- CONV_TYPES = (nn.Conv2d, nn.Conv3d)
- class Classifier(nn.Module):
- @abstractmethod
- def compute_loss(self, pred_logits: Tensor, targets: Tensor, **kwargs) -> Tensor:
- """
- Compute classification loss (cross entropy loss)
- Args:
- pred_logits (Tensor): predicted logits
- targets (Tensor): classification targets
- Returns:
- Tensor: classification loss
- """
- raise NotImplementedError
- @abstractmethod
- def box_logits_to_probs(self, box_logits: Tensor) -> Tensor:
- """
- Convert bounding box logits to probabilities
- Args:
- box_logits (Tensor): bounding box logits [N, C], C=number of classes
- Returns:
- Tensor: probabilities
- """
- raise NotImplementedError
- class BaseClassifier(Classifier):
- def __init__(self,
- conv,
- in_channels: int,
- internal_channels: int,
- num_classes: int,
- anchors_per_pos: int,
- num_levels: int,
- num_convs: int = 3,
- add_norm: bool = True,
- **kwargs
- ):
- """
- Base class to build classifier heads with typical conv structure
- conv(in, internal) -> num_convs x conv(internal, internal) ->
- conv(internal, out)
- Args:
- conv: Convolution modules which handles a single layer
- in_channels: number of input channels
- internal_channels: number of channels internally used
- num_classes: number of foreground classes
- anchors_per_pos: number of anchors per position
- num_levels: number of decoder levels which are passed through the
- classifier
- num_convs: number of convolutions
- input_conv -> num_convs -> output_convs
- add_norm: en-/disable normalization layers in internal layers
- kwargs: keyword arguments passed to first and internal convolutions
- Notes:
- `self.loss` needs to be overwritten in subclasses
- `self.logits_convert_fn` needs to be overwritten in subclasses
- """
- super().__init__()
- self.dim = conv.dim
- self.num_levels = num_levels
- self.num_convs = num_convs
- self.num_classes = num_classes
- self.anchors_per_pos = anchors_per_pos
- self.in_channels = in_channels
- self.internal_channels = internal_channels
- self.conv_internal = self.build_conv_internal(conv, add_norm=add_norm, **kwargs)
- self.conv_out = self.build_conv_out(conv)
- self.loss: Optional[nn.Module] = None
- self.logits_convert_fn: Optional[nn.Module] = None
- self.init_weights()
- def build_conv_internal(self, conv, **kwargs):
- """
- Build internal convolutions
- """
- _conv_internal = nn.Sequential()
- _conv_internal.add_module(
- name="c_in",
- module=conv(
- self.in_channels,
- self.internal_channels,
- kernel_size=3,
- stride=1,
- padding=1,
- **kwargs,
- ))
- for i in range(self.num_convs):
- _conv_internal.add_module(
- name=f"c_internal{i}",
- module=conv(
- self.internal_channels,
- self.internal_channels,
- kernel_size=3,
- stride=1,
- padding=1,
- **kwargs,
- ))
- return _conv_internal
- def build_conv_out(self, conv):
- """
- Build final convolutions
- """
- out_channels = self.num_classes * self.anchors_per_pos
- return conv(
- self.internal_channels,
- out_channels,
- kernel_size=3,
- stride=1,
- padding=1,
- add_norm=False,
- add_act=False,
- bias=True,
- )
- def forward(self,
- x: torch.Tensor,
- level: int,
- **kwargs,
- ) -> torch.Tensor:
- """
- Forward input
- Args:
- x (torch.Tensor): input feature map of size (N x C x Y x X x Z)
- Returns:
- torch.Tensor: classification logits for each anchor
- (N x anchors x num_classes)
- """
- class_logits = self.conv_out(self.conv_internal(x))
- axes = (0, 2, 3, 1) if self.dim == 2 else (0, 2, 3, 4, 1)
- class_logits = class_logits.permute(*axes)
- class_logits = class_logits.contiguous()
- class_logits = class_logits.view(x.size()[0], -1, self.num_classes)
- return class_logits
- def compute_loss(self, pred_logits: Tensor, targets: Tensor, **kwargs) -> Tensor:
- """
- Base classifier with cross entropy loss (in general hard negative
- example mining should be done before this)
- Args:
- pred_logits (Tensor): predicted logits
- targets (Tensor): classification targets
- Returns:
- Tensor: classification loss
- """
- return self.loss(pred_logits, targets.long(), **kwargs)
- def box_logits_to_probs(self, box_logits: Tensor) -> Tensor:
- """
- Convert bounding box logits to probabilities
- Args:
- box_logits (Tensor): bounding box logits [N, C]
- N = number of anchors, C=number of foreground classes
- Returns:
- Tensor: probabilities
- """
- return self.logits_convert_fn(box_logits)
- def init_weights(self) -> None:
- """
- Init weights with prior prob
- """
- if self.prior_prob is not None:
- logger.info(f"Init classifier weights: prior prob {self.prior_prob}")
- for layer in self.modules():
- if isinstance(layer, CONV_TYPES):
- torch.nn.init.normal_(layer.weight, mean=0, std=0.01)
- if layer.bias is not None:
- torch.nn.init.constant_(layer.bias, 0)
- # Use prior in model initialization to improve stability
- bias_value = -math.log((1 - self.prior_prob) / self.prior_prob)
- for layer in self.conv_out.modules():
- if isinstance(layer, CONV_TYPES):
- torch.nn.init.constant_(layer.bias, bias_value)
- else:
- logger.info("Init classifier weights: conv default")
- class BCECLassifier(BaseClassifier):
- def __init__(self,
- conv,
- in_channels: int,
- internal_channels: int,
- num_classes: int,
- anchors_per_pos: int,
- num_levels: int,
- num_convs: int = 3,
- add_norm: bool = True,
- prior_prob: Optional[float] = None,
- weight: Optional[Tensor] = None,
- reduction: str = "mean",
- smoothing: float = 0.0,
- loss_weight: float = 1.,
- **kwargs
- ):
- """
- Classifier Head with sigmoid based BCE loss computation and prio
- prob weight init
- conv(in, internal) -> num_convs x conv(internal, internal) ->
- conv(internal, out)
- Args:
- conv: Convolution modules which handles a single layer
- in_channels: number of input channels
- internal_channels: number of channels internally used
- num_classes: number of foreground classes
- anchors_per_pos: number of anchors per position
- num_levels: number of decoder levels which are passed through the
- classifier
- num_convs: number of convolutions
- input_conv -> num_convs -> output_convs
- add_norm: en-/disable normalization layers in internal layers
- prior_prob: initialize final conv with given prior probability
- weight: weight in BCEWithLogitsLoss (see pytorch for more info)
- reduction: reduction to apply to loss. 'sum' | 'mean' | 'none'
- smoothing: label smoothing
- loss_weight: scalar to balance multiple losses
- kwargs: keyword arguments passed to first and internal convolutions
- """
- self.prior_prob = prior_prob
- super().__init__(
- conv=conv,
- in_channels=in_channels,
- num_convs=num_convs,
- add_norm=add_norm,
- internal_channels=internal_channels,
- num_classes=num_classes,
- anchors_per_pos=anchors_per_pos,
- num_levels=num_levels,
- **kwargs,
- )
- self.loss = BCEWithLogitsLossOneHot(
- num_classes=num_classes,
- weight=weight,
- reduction=reduction,
- smoothing=smoothing,
- loss_weight=loss_weight,
- )
- self.logits_convert_fn = nn.Sigmoid()
- class CEClassifier(BaseClassifier):
- def __init__(self,
- conv,
- in_channels: int,
- internal_channels: int,
- num_classes: int,
- anchors_per_pos: int,
- num_levels: int,
- num_convs: int = 3,
- add_norm: bool = True,
- prior_prob: Optional[float] = None,
- weight: Optional[Tensor] = None,
- reduction: str = "mean",
- loss_weight: float = 1.,
- **kwargs
- ):
- """
- Classifier Head with sigmoid based BCE loss computation and prio
- prob weight init
- conv(in, internal) -> num_convs x conv(internal, internal) ->
- conv(internal, out)
- Args:
- conv: Convolution modules which handles a single layer
- in_channels: number of input channels
- internal_channels: number of channels internally used
- num_classes: number of foreground classes
- anchors_per_pos: number of anchors per position
- num_levels: number of decoder levels which are passed through the
- classifier
- num_convs: number of convolutions
- input_conv -> num_convs -> output_convs
- add_norm: en-/disable normalization layers in internal layers
- prior_prob: initialize final conv with given prior probability
- weight: weight in cross entrpoy loss (see pytorch for more info)
- reduction: reduction to apply to loss. 'sum' | 'mean' | 'none'
- loss_weight: scalar to balance multiple losses
- kwargs: keyword arguments passed to first and internal convolutions
- """
- self.prior_prob = prior_prob
- super().__init__(
- conv=conv,
- in_channels=in_channels,
- num_convs=num_convs,
- add_norm=add_norm,
- internal_channels=internal_channels,
- num_classes=num_classes + 1, # add one channel for background
- anchors_per_pos=anchors_per_pos,
- num_levels=num_levels,
- **kwargs,
- )
- self.loss = CrossEntropyLoss(
- weight=weight,
- reduction=reduction,
- loss_weight=loss_weight,
- )
- self.logits_convert_fn = nn.Softmax(dim=1)
- def box_logits_to_probs(self, box_logits: Tensor) -> Tensor:
- """
- Convert bounding box logits to probabilities
- Args:
- box_logits (Tensor): bounding box logits [N, C], C=number of classes
- Returns:
- Tensor: probabilities
- """
- return self.logits_convert_fn(box_logits)[:, 1:] # remove background predictions
- class FocalClassifier(BaseClassifier):
- def __init__(self,
- conv,
- in_channels: int,
- internal_channels: int,
- num_classes: int,
- anchors_per_pos: int,
- num_levels: int,
- num_convs: int = 3,
- add_norm: bool = True,
- prior_prob: Optional[float] = None,
- gamma: float = 2,
- alpha: float = -1,
- reduction: str = "sum",
- loss_weight: float = 1.,
- **kwargs
- ):
- """
- Classifier Head with sigmoid based BCE loss computation and
- prio prob weight init
- conv(in, internal) -> num_convs x conv(internal, internal) ->
- conv(internal, out)
- Args:
- conv: Convolution modules which handles a single layer
- in_channels: number of input channels
- internal_channels: number of channels internally used
- num_classes: number of foreground classes
- anchors_per_pos: number of anchors per position
- num_levels: number of decoder levels which are passed through the
- classifier
- num_convs: number of convolutions
- input_conv -> num_convs -> output_convs
- add_norm: en-/disable normalization layers in internal layers
- prior_prob: initialize final conv with given prior probability
- gamma: focal loss gamma
- alpha: focal loss alpha
- reduction: reduction to apply to loss. 'sum' | 'mean' | 'none'
- loss_weight: scalar to balance multiple losses
- kwargs: keyword arguments passed to first and internal convolutions
- """
- self.prior_prob = prior_prob
- super().__init__(
- conv=conv,
- in_channels=in_channels,
- num_convs=num_convs,
- add_norm=add_norm,
- internal_channels=internal_channels,
- num_classes=num_classes,
- anchors_per_pos=anchors_per_pos,
- num_levels=num_levels,
- **kwargs,
- )
- self.loss = FocalLossWithLogits(
- gamma=gamma,
- alpha=alpha,
- reduction=reduction,
- loss_weight=loss_weight,
- )
- self.logits_convert_fn = nn.Sigmoid()
- ClassifierType = TypeVar('ClassifierType', bound=Classifier)
classifier.py at commit 97a58f3, no license · at the source
Overview
- Computer Vision and Robotics Institute, University of Girona, Girona, Catalonia Spain
- Department of Neurology, Hospital Universitari Dr Josep Trueta - Institut d’Investigació Biomèdica de Girona, Girona, Catalonia Spain
Abstract
Large vessel occlusions (LVOs) are blockages in the brain’s major arteries that can cause severe neurological damage. Rapid and accurate detection using computed tomography angiography (CTA) is critical for timely stroke treatment. Here, we present a fully automated approach that detects LVOs and classifies the affected vessel simultaneously. Our method incorporates a spatial prior by using Circle of Willis (CoW) segmentation as additional input, guiding the model to anatomically relevant regions. We evaluated the two strategies, the global approach using the full CTA volume, and the local one focused on CoW regions. Both achieved high performance. Detection sensitivity was 0.97 at 0.20 false positives per image for the global approach, and 0.97 at 0.13 false positives for the local approach. Classification accuracy reached 94% and 91% for global and local strategies, respectively. Importantly, the local approach was 3.3× faster, offering a computationally efficient solution, a critical advantage in acute stroke care, where every minute impacts patient outcomes.
Reproduced under the paper's license (CC BY), from the paper cited above.
Repositories
Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.
MIC-DKFZ/nnDetection
97a58f3110b71caf1b4bcc1851e67cf11e987fc5, 27 October 2025Availability: 1 check, the latest on 26 September 2026: the link answers
- 26 September 2026: the link answers
167 files
- nndet/
__init__.py , Python, 1 line - nndet/
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__init__.py , Python, 1 line - tests/
test_imports.py , Python, 18 lines - README.md, Text, 598 lines
NIC-VICOROB/CoW-multiclass-segmentation-TopCoW24
e47cc66e9211d3dab8400ffac599c3523d0f08d9, 3 February 2026Availability: 1 check, the latest on 26 September 2026: the link answers
- 26 September 2026: the link answers
573 files
- algo_submission/
task-1-seg/ , Python, 157 linesinference.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ __init__.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ batch_running/ __init__.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ batch_running/ benchmarking/ __init__.py - algo_submission/
task-1-seg/ , Python, 41 linesnnunetv2/ batch_running/ benchmarking/ generate_benchmarking_co mmands.py - algo_submission/
task-1-seg/ , Python, 70 linesnnunetv2/ batch_running/ benchmarking/ summarize_benchmark_resu lts.py - algo_submission/
task-1-seg/ , Python, 112 linesnnunetv2/ batch_running/ collect_results_custom_D ecathlon.py - algo_submission/
task-1-seg/ , Python, 18 linesnnunetv2/ batch_running/ collect_results_custom_D ecathlon_2d.py - algo_submission/
task-1-seg/ , Python, 105 linesnnunetv2/ batch_running/ generate_lsf_runs_custom Decathlon.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ batch_running/ release_trainings/ __init__.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ batch_running/ release_trainings/ nnunetv2_v1/ __init__.py - algo_submission/
task-1-seg/ , Python, 113 linesnnunetv2/ batch_running/ release_trainings/ nnunetv2_v1/ collect_results.py - algo_submission/
task-1-seg/ , Python, 93 linesnnunetv2/ batch_running/ release_trainings/ nnunetv2_v1/ generate_lsf_commands.py - algo_submission/
task-1-seg/ , Python, 10 linesnnunetv2/ configuration.py - algo_submission/
task-1-seg/ , Python, 114 linesnnunetv2/ dataset_conversion/ Dataset027_ACDC.py - algo_submission/
task-1-seg/ , Python, 110 linesnnunetv2/ dataset_conversion/ Dataset042_BraTS18.py - algo_submission/
task-1-seg/ , Python, 110 linesnnunetv2/ dataset_conversion/ Dataset043_BraTS19.py - algo_submission/
task-1-seg/ , Python, 85 linesnnunetv2/ dataset_conversion/ Dataset073_Fluo_C3DH_A54 9_SIM.py - algo_submission/
task-1-seg/ , Python, 198 linesnnunetv2/ dataset_conversion/ Dataset114_MNMs.py - algo_submission/
task-1-seg/ , Python, 61 linesnnunetv2/ dataset_conversion/ Dataset115_EMIDEC.py - algo_submission/
task-1-seg/ , Python, 87 linesnnunetv2/ dataset_conversion/ Dataset120_RoadSegmentat ion.py - algo_submission/
task-1-seg/ , Python, 98 linesnnunetv2/ dataset_conversion/ Dataset137_BraTS21.py - algo_submission/
task-1-seg/ , Python, 70 linesnnunetv2/ dataset_conversion/ Dataset218_Amos2022_task 1.py - algo_submission/
task-1-seg/ , Python, 65 linesnnunetv2/ dataset_conversion/ Dataset219_Amos2022_task 2.py - algo_submission/
task-1-seg/ , Python, 50 linesnnunetv2/ dataset_conversion/ Dataset220_KiTS2023.py - algo_submission/
task-1-seg/ , Python, 70 linesnnunetv2/ dataset_conversion/ Dataset221_AutoPETII_202 3.py - algo_submission/
task-1-seg/ , Python, 59 linesnnunetv2/ dataset_conversion/ Dataset223_AMOS2022postC hallenge.py - algo_submission/
task-1-seg/ , Python, 32 linesnnunetv2/ dataset_conversion/ Dataset988_dummyDataset4 .py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ dataset_conversion/ __init__.py - algo_submission/
task-1-seg/ , Python, 132 linesnnunetv2/ dataset_conversion/ convert_MSD_dataset.py - algo_submission/
task-1-seg/ , Python, 53 linesnnunetv2/ dataset_conversion/ convert_raw_dataset_from _old_nnunet_format.py - algo_submission/
task-1-seg/ , Python, 75 linesnnunetv2/ dataset_conversion/ datasets_for_integration _tests/ Dataset996_IntegrationTe st_Hippocampus_regions_i gnore.py - algo_submission/
task-1-seg/ , Python, 37 linesnnunetv2/ dataset_conversion/ datasets_for_integration _tests/ Dataset997_IntegrationTe st_Hippocampus_regions.p y - algo_submission/
task-1-seg/ , Python, 33 linesnnunetv2/ dataset_conversion/ datasets_for_integration _tests/ Dataset998_IntegrationTe st_Hippocampus_ignore.py - algo_submission/
task-1-seg/ , Python, 27 linesnnunetv2/ dataset_conversion/ datasets_for_integration _tests/ Dataset999_IntegrationTe st_Hippocampus.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ dataset_conversion/ datasets_for_integration _tests/ __init__.py - algo_submission/
task-1-seg/ , Python, 103 linesnnunetv2/ dataset_conversion/ generate_dataset_json.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ ensembling/ __init__.py - algo_submission/
task-1-seg/ , Python, 206 linesnnunetv2/ ensembling/ ensemble.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ evaluation/ __init__.py - algo_submission/
task-1-seg/ , Python, 58 linesnnunetv2/ evaluation/ accumulate_cv_results.py - algo_submission/
task-1-seg/ , Python, 264 linesnnunetv2/ evaluation/ evaluate_predictions.py - algo_submission/
task-1-seg/ , Python, 333 linesnnunetv2/ evaluation/ find_best_configuration. py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ experiment_planning/ __init__.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ experiment_planning/ dataset_fingerprint/ __init__.py - algo_submission/
task-1-seg/ , Python, 210 linesnnunetv2/ experiment_planning/ dataset_fingerprint/ fingerprint_extractor.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ experiment_planning/ experiment_planners/ __init__.py - algo_submission/
task-1-seg/ , Python, 593 linesnnunetv2/ experiment_planning/ experiment_planners/ default_experiment_plann er.py - algo_submission/
task-1-seg/ , Python, 108 linesnnunetv2/ experiment_planning/ experiment_planners/ network_topology.py - algo_submission/
task-1-seg/ , Python, 235 linesnnunetv2/ experiment_planning/ experiment_planners/ resencUNet_planner.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ experiment_planning/ experiment_planners/ residual_unets/ __init__.py - algo_submission/
task-1-seg/ , Python, 313 linesnnunetv2/ experiment_planning/ experiment_planners/ residual_unets/ residual_encoder_unet_pl anners.py - algo_submission/
task-1-seg/ , Python, 150 linesnnunetv2/ experiment_planning/ plan_and_preprocess_api. py - algo_submission/
task-1-seg/ , Python, 204 linesnnunetv2/ experiment_planning/ plan_and_preprocess_entr ypoints.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ experiment_planning/ plans_for_pretraining/ __init__.py - algo_submission/
task-1-seg/ , Python, 83 linesnnunetv2/ experiment_planning/ plans_for_pretraining/ move_plans_between_datas ets.py - algo_submission/
task-1-seg/ , Python, 233 linesnnunetv2/ experiment_planning/ verify_dataset_integrity .py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ imageio/ __init__.py - algo_submission/
task-1-seg/ , Python, 107 linesnnunetv2/ imageio/ base_reader_writer.py - algo_submission/
task-1-seg/ , Python, 73 linesnnunetv2/ imageio/ natural_image_reader_wri ter.py - algo_submission/
task-1-seg/ , Python, 208 linesnnunetv2/ imageio/ nibabel_reader_writer.py - algo_submission/
task-1-seg/ , Python, 79 linesnnunetv2/ imageio/ reader_writer_registry.p y - algo_submission/
task-1-seg/ , Python, 130 linesnnunetv2/ imageio/ simpleitk_reader_writer. py - algo_submission/
task-1-seg/ , Python, 100 linesnnunetv2/ imageio/ tif_reader_writer.py - algo_submission/
task-1-seg/ , Python, 197 linesnnunetv2/ inference/ JHU_inference.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ inference/ __init__.py - algo_submission/
task-1-seg/ , Python, 313 linesnnunetv2/ inference/ data_iterators.py - algo_submission/
task-1-seg/ , Python, 102 linesnnunetv2/ inference/ examples.py - algo_submission/
task-1-seg/ , Python, 146 linesnnunetv2/ inference/ export_prediction.py - algo_submission/
task-1-seg/ , Python, 947 linesnnunetv2/ inference/ predict_from_raw_data.py - algo_submission/
task-1-seg/ , Python, 65 linesnnunetv2/ inference/ sliding_window_predictio n.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ model_sharing/ __init__.py - algo_submission/
task-1-seg/ , Python, 61 linesnnunetv2/ model_sharing/ entry_points.py - algo_submission/
task-1-seg/ , Python, 47 linesnnunetv2/ model_sharing/ model_download.py - algo_submission/
task-1-seg/ , Python, 124 linesnnunetv2/ model_sharing/ model_export.py - algo_submission/
task-1-seg/ , Python, 8 linesnnunetv2/ model_sharing/ model_import.py - algo_submission/
task-1-seg/ , Python, 188 linesnnunetv2/ nets/ ResidualAttUNet_3d.py - algo_submission/
task-1-seg/ , Python, 39 linesnnunetv2/ paths.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ postprocessing/ __init__.py - algo_submission/
task-1-seg/ , Python, 362 linesnnunetv2/ postprocessing/ remove_connected_compone nts.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ preprocessing/ __init__.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ preprocessing/ cropping/ __init__.py - algo_submission/
task-1-seg/ , Python, 43 linesnnunetv2/ preprocessing/ cropping/ cropping.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ preprocessing/ normalization/ __init__.py - algo_submission/
task-1-seg/ , Python, 98 linesnnunetv2/ preprocessing/ normalization/ default_normalization_sc hemes.py - algo_submission/
task-1-seg/ , Python, 26 linesnnunetv2/ preprocessing/ normalization/ map_channel_name_to_norm alization.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ preprocessing/ preprocessors/ __init__.py - algo_submission/
task-1-seg/ , Python, 297 linesnnunetv2/ preprocessing/ preprocessors/ default_preprocessor.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ preprocessing/ resampling/ __init__.py - algo_submission/
task-1-seg/ , Python, 189 linesnnunetv2/ preprocessing/ resampling/ default_resampling.py - algo_submission/
task-1-seg/ , Python, 173 linesnnunetv2/ preprocessing/ resampling/ resample_torch.py - algo_submission/
task-1-seg/ , Jupyter, 66 linesnnunetv2/ preprocessing/ resampling/ resampling_custom.ipynb - algo_submission/
task-1-seg/ , Python, 15 linesnnunetv2/ preprocessing/ resampling/ utils.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ run/ __init__.py - algo_submission/
task-1-seg/ , Python, 71 linesnnunetv2/ run/ load_pretrained_weights. py - algo_submission/
task-1-seg/ , Python, 285 linesnnunetv2/ run/ run_training.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ tests/ __init__.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ tests/ integration_tests/ __init__.py - algo_submission/
task-1-seg/ , Python, 33 linesnnunetv2/ tests/ integration_tests/ add_lowres_and_cascade.p y - algo_submission/
task-1-seg/ , Python, 19 linesnnunetv2/ tests/ integration_tests/ cleanup_integration_test .py - algo_submission/
task-1-seg/ , Shell, 10 linesnnunetv2/ tests/ integration_tests/ lsf_commands.sh - algo_submission/
task-1-seg/ , Shell, 18 linesnnunetv2/ tests/ integration_tests/ prepare_integration_test s.sh - algo_submission/
task-1-seg/ , Shell, 27 linesnnunetv2/ tests/ integration_tests/ run_integration_test.sh - algo_submission/
task-1-seg/ , Python, 75 linesnnunetv2/ tests/ integration_tests/ run_integration_test_bes tconfig_inference.py - algo_submission/
task-1-seg/ , Shell, 1 linennunetv2/ tests/ integration_tests/ run_integration_test_tra iningOnly_DDP.sh - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ training/ __init__.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ training/ data_augmentation/ __init__.py - algo_submission/
task-1-seg/ , Python, 24 linesnnunetv2/ training/ data_augmentation/ compute_initial_patch_si ze.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ training/ data_augmentation/ custom_transforms/ __init__.py - algo_submission/
task-1-seg/ , Python, 136 linesnnunetv2/ training/ data_augmentation/ custom_transforms/ cascade_transforms.py - algo_submission/
task-1-seg/ , Python, 55 linesnnunetv2/ training/ data_augmentation/ custom_transforms/ deep_supervision_donwsam pling.py - algo_submission/
task-1-seg/ , Python, 22 linesnnunetv2/ training/ data_augmentation/ custom_transforms/ masking.py - algo_submission/
task-1-seg/ , Python, 32 linesnnunetv2/ training/ data_augmentation/ custom_transforms/ region_based_training.py - algo_submission/
task-1-seg/ , Python, 35 linesnnunetv2/ training/ data_augmentation/ custom_transforms/ skeletonization.py - algo_submission/
task-1-seg/ , Python, 45 linesnnunetv2/ training/ data_augmentation/ custom_transforms/ transforms_for_dummy_2d. py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ training/ dataloading/ __init__.py - algo_submission/
task-1-seg/ , Python, 142 linesnnunetv2/ training/ dataloading/ base_data_loader.py - algo_submission/
task-1-seg/ , Python, 118 linesnnunetv2/ training/ dataloading/ data_loader_2d.py - algo_submission/
task-1-seg/ , Python, 113 linesnnunetv2/ training/ dataloading/ data_loader_2d_skel.py - algo_submission/
task-1-seg/ , Python, 152 linesnnunetv2/ training/ dataloading/ data_loader_3d.py - algo_submission/
task-1-seg/ , Python, 91 linesnnunetv2/ training/ dataloading/ data_loader_3d_skel.py - algo_submission/
task-1-seg/ , Python, 146 linesnnunetv2/ training/ dataloading/ nnunet_dataset.py - algo_submission/
task-1-seg/ , Python, 82 linesnnunetv2/ training/ dataloading/ utils.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ training/ logging/ __init__.py - algo_submission/
task-1-seg/ , Python, 103 linesnnunetv2/ training/ logging/ nnunet_logger.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ training/ loss/ __init__.py - algo_submission/
task-1-seg/ , Python, 300 linesnnunetv2/ training/ loss/ compound_losses.py - algo_submission/
task-1-seg/ , Python, 30 linesnnunetv2/ training/ loss/ deep_supervision.py - algo_submission/
task-1-seg/ , Python, 356 linesnnunetv2/ training/ loss/ dice.py - algo_submission/
task-1-seg/ , Python, 91 linesnnunetv2/ training/ loss/ focal_loss.py - algo_submission/
task-1-seg/ , Python, 32 linesnnunetv2/ training/ loss/ robust_ce_loss.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ training/ lr_scheduler/ __init__.py - algo_submission/
task-1-seg/ , Python, 20 linesnnunetv2/ training/ lr_scheduler/ polylr.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ training/ nnUNetTrainer/ __init__.py - algo_submission/
task-1-seg/ , Python, 1,509 linesnnunetv2/ training/ nnUNetTrainer/ nnUNetTrainer.py - algo_submission/
task-1-seg/ , Python, 164 linesnnunetv2/ training/ nnUNetTrainer/ nnUNetTrainerResAttUNet. py - algo_submission/
task-1-seg/ , Python, 1,475 linesnnunetv2/ training/ nnUNetTrainer/ nnUNetTrainer_2.py - algo_submission/
task-1-seg/ , Python, 1,443 linesnnunetv2/ training/ nnUNetTrainer/ nnUNetTrainer_epvs.py - algo_submission/
task-1-seg/ , Python, 1,443 linesnnunetv2/ training/ nnUNetTrainer/ nnUNetTrainer_numpatches .py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ training/ nnUNetTrainer/ variants/ __init__.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ training/ nnUNetTrainer/ variants/ benchmarking/ __init__.py - algo_submission/
task-1-seg/ , Python, 70 linesnnunetv2/ training/ nnUNetTrainer/ variants/ benchmarking/ nnUNetTrainerBenchmark_5 epochs.py - algo_submission/
task-1-seg/ , Python, 65 linesnnunetv2/ training/ nnUNetTrainer/ variants/ benchmarking/ nnUNetTrainerBenchmark_5 epochs_noDataLoading.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ training/ nnUNetTrainer/ variants/ data_augmentation/ __init__.py - algo_submission/
task-1-seg/ , Python, 854 linesnnunetv2/ training/ nnUNetTrainer/ variants/ data_augmentation/ nnUNetTrainerDA5.py - algo_submission/
task-1-seg/ , Python, 268 linesnnunetv2/ training/ nnUNetTrainer/ variants/ data_augmentation/ nnUNetTrainerDAOrd0.py - algo_submission/
task-1-seg/ , Python, 35 linesnnunetv2/ training/ nnUNetTrainer/ variants/ data_augmentation/ nnUNetTrainerNoDA.py - algo_submission/
task-1-seg/ , Python, 28 linesnnunetv2/ training/ nnUNetTrainer/ variants/ data_augmentation/ nnUNetTrainerNoMirroring .py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ training/ nnUNetTrainer/ variants/ loss/ __init__.py - algo_submission/
task-1-seg/ , Python, 41 linesnnunetv2/ training/ nnUNetTrainer/ variants/ loss/ nnUNetTrainerCELoss.py - algo_submission/
task-1-seg/ , Python, 60 linesnnunetv2/ training/ nnUNetTrainer/ variants/ loss/ nnUNetTrainerDiceLoss.py - algo_submission/
task-1-seg/ , Python, 457 linesnnunetv2/ training/ nnUNetTrainer/ variants/ loss/ nnUNetTrainerSkeletonRec all.py - algo_submission/
task-1-seg/ , Python, 464 linesnnunetv2/ training/ nnUNetTrainer/ variants/ loss/ nnUNetTrainerSkeletonRec allBinDice.py - algo_submission/
task-1-seg/ , Python, 76 linesnnunetv2/ training/ nnUNetTrainer/ variants/ loss/ nnUNetTrainerTopkLoss.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ training/ nnUNetTrainer/ variants/ lr_schedule/ __init__.py - algo_submission/
task-1-seg/ , Python, 13 linesnnunetv2/ training/ nnUNetTrainer/ variants/ lr_schedule/ nnUNetTrainerCosAnneal.p y - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ training/ nnUNetTrainer/ variants/ network_architecture/ __init__.py - algo_submission/
task-1-seg/ , Python, 32 linesnnunetv2/ training/ nnUNetTrainer/ variants/ network_architecture/ nnUNetTrainerBN.py - algo_submission/
task-1-seg/ , Python, 16 linesnnunetv2/ training/ nnUNetTrainer/ variants/ network_architecture/ nnUNetTrainerNoDeepSuper vision.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ training/ nnUNetTrainer/ variants/ optimizer/ __init__.py - algo_submission/
task-1-seg/ , Python, 58 linesnnunetv2/ training/ nnUNetTrainer/ variants/ optimizer/ nnUNetTrainerAdam.py - algo_submission/
task-1-seg/ , Python, 66 linesnnunetv2/ training/ nnUNetTrainer/ variants/ optimizer/ nnUNetTrainerAdan.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ training/ nnUNetTrainer/ variants/ sampling/ __init__.py - algo_submission/
task-1-seg/ , Python, 84 linesnnunetv2/ training/ nnUNetTrainer/ variants/ sampling/ nnUNetTrainer_probabilis ticOversampling.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ training/ nnUNetTrainer/ variants/ training_length/ __init__.py - algo_submission/
task-1-seg/ , Python, 76 linesnnunetv2/ training/ nnUNetTrainer/ variants/ training_length/ nnUNetTrainer_Xepochs.py - algo_submission/
task-1-seg/ , Python, 60 linesnnunetv2/ training/ nnUNetTrainer/ variants/ training_length/ nnUNetTrainer_Xepochs_No Mirroring.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ utilities/ __init__.py - algo_submission/
task-1-seg/ , Python, 24 linesnnunetv2/ utilities/ collate_outputs.py - algo_submission/
task-1-seg/ , Python, 16 linesnnunetv2/ utilities/ crossval_split.py - algo_submission/
task-1-seg/ , Python, 74 linesnnunetv2/ utilities/ dataset_name_id_conversi on.py - algo_submission/
task-1-seg/ , Python, 49 linesnnunetv2/ utilities/ ddp_allgather.py - algo_submission/
task-1-seg/ , Python, 44 linesnnunetv2/ utilities/ default_n_proc_DA.py - algo_submission/
task-1-seg/ , Python, 123 linesnnunetv2/ utilities/ file_path_utilities.py - algo_submission/
task-1-seg/ , Python, 24 linesnnunetv2/ utilities/ find_class_by_name.py - algo_submission/
task-1-seg/ , Python, 43 linesnnunetv2/ utilities/ get_network_from_plans.p y - algo_submission/
task-1-seg/ , Python, 27 linesnnunetv2/ utilities/ helpers.py - algo_submission/
task-1-seg/ , Python, 60 linesnnunetv2/ utilities/ json_export.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ utilities/ label_handling/ __init__.py - algo_submission/
task-1-seg/ , Python, 322 linesnnunetv2/ utilities/ label_handling/ label_handling.py - algo_submission/
task-1-seg/ , Python, 12 linesnnunetv2/ utilities/ network_initialization.p y - algo_submission/
task-1-seg/ , Python, 275 linesnnunetv2/ utilities/ overlay_plots.py - algo_submission/
task-1-seg/ , Python, 1 linennunetv2/ utilities/ plans_handling/ __init__.py - algo_submission/
task-1-seg/ , Python, 339 linesnnunetv2/ utilities/ plans_handling/ plans_handler.py - algo_submission/
task-1-seg/ , Python, 180 linesnnunetv2/ utilities/ sam.py - algo_submission/
task-1-seg/ , Python, 69 linesnnunetv2/ utilities/ utils.py - algo_submission/
task-1-seg/ , Python, 270 linespost_processings.py - algo_submission/
task-1-seg/ , Shell, 38 linessave.sh - algo_submission/
task-1-seg/ , Shell, 119 linestest_run.sh - algo_submission/
task-1-seg/ , Python, 17 linestorch_utilities.py - algo_submission/
task-1-seg/ , Python, 176 linesyour_algorithm.py - algo_submission/
task-2-box/ , Python, 145 linesinference.py - algo_submission/
task-2-box/ , Python, 1 linennunetv2/ __init__.py - algo_submission/
task-2-box/ , Python, 1 linennunetv2/ batch_running/ __init__.py - algo_submission/
task-2-box/ , Python, 1 linennunetv2/ batch_running/ benchmarking/ __init__.py - algo_submission/
task-2-box/ , Python, 41 linesnnunetv2/ batch_running/ benchmarking/ generate_benchmarking_co mmands.py - algo_submission/
task-2-box/ , Python, 70 linesnnunetv2/ batch_running/ benchmarking/ summarize_benchmark_resu lts.py - algo_submission/
task-2-box/ , Python, 112 linesnnunetv2/ batch_running/ collect_results_custom_D ecathlon.py - algo_submission/
task-2-box/ , Python, 18 linesnnunetv2/ batch_running/ collect_results_custom_D ecathlon_2d.py - algo_submission/
task-2-box/ , Python, 105 linesnnunetv2/ batch_running/ generate_lsf_runs_custom Decathlon.py - algo_submission/
task-2-box/ , Python, 1 linennunetv2/ batch_running/ release_trainings/ __init__.py - algo_submission/
task-2-box/ , Python, 1 linennunetv2/ batch_running/ release_trainings/ nnunetv2_v1/ __init__.py - algo_submission/
task-2-box/ , Python, 113 linesnnunetv2/ batch_running/ release_trainings/ nnunetv2_v1/ collect_results.py - algo_submission/
task-2-box/ , Python, 93 linesnnunetv2/ batch_running/ release_trainings/ nnunetv2_v1/ generate_lsf_commands.py - algo_submission/
task-2-box/ , Python, 10 linesnnunetv2/ configuration.py - algo_submission/
task-2-box/ , Python, 114 linesnnunetv2/ dataset_conversion/ Dataset027_ACDC.py - algo_submission/
task-2-box/ , Python, 110 linesnnunetv2/ dataset_conversion/ Dataset042_BraTS18.py - algo_submission/
task-2-box/ , Python, 110 linesnnunetv2/ dataset_conversion/ Dataset043_BraTS19.py - algo_submission/
task-2-box/ , Python, 85 linesnnunetv2/ dataset_conversion/ Dataset073_Fluo_C3DH_A54 9_SIM.py - algo_submission/
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task-2-box/ , Python, 204 linesnnunetv2/ experiment_planning/ plan_and_preprocess_entr ypoints.py - algo_submission/
task-2-box/ , Python, 1 linennunetv2/ experiment_planning/ plans_for_pretraining/ __init__.py - algo_submission/
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task-2-box/ , Python, 197 linesnnunetv2/ inference/ JHU_inference.py - algo_submission/
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task-2-box/ , Python, 188 linesnnunetv2/ nets/ ResidualAttUNet_3d.py - algo_submission/
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task-2-box/ , Python, 26 linesnnunetv2/ preprocessing/ normalization/ map_channel_name_to_norm alization.py - algo_submission/
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task-2-box/ , Python, 1 linennunetv2/ preprocessing/ resampling/ __init__.py - algo_submission/
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task-2-box/ , Jupyter, 66 linesnnunetv2/ preprocessing/ resampling/ resampling_custom.ipynb - algo_submission/
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task-2-box/ , Python, 1 linennunetv2/ run/ __init__.py - algo_submission/
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task-2-box/ , Python, 285 linesnnunetv2/ run/ run_training.py - algo_submission/
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task-2-box/ , Python, 19 linesnnunetv2/ tests/ integration_tests/ cleanup_integration_test .py - algo_submission/
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task-2-box/ , Python, 75 linesnnunetv2/ tests/ integration_tests/ run_integration_test_bes tconfig_inference.py - algo_submission/
task-2-box/ , Shell, 1 linennunetv2/ tests/ integration_tests/ run_integration_test_tra iningOnly_DDP.sh - algo_submission/
task-2-box/ , Python, 1 linennunetv2/ training/ __init__.py - algo_submission/
task-2-box/ , Python, 1 linennunetv2/ training/ data_augmentation/ __init__.py - algo_submission/
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task-2-box/ , Python, 32 linesnnunetv2/ training/ data_augmentation/ custom_transforms/ region_based_training.py - algo_submission/
task-2-box/ , Python, 35 linesnnunetv2/ training/ data_augmentation/ custom_transforms/ skeletonization.py - algo_submission/
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task-2-box/ , Python, 1 linennunetv2/ training/ dataloading/ __init__.py - algo_submission/
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task-2-box/ , Python, 103 linesnnunetv2/ training/ logging/ nnunet_logger.py - algo_submission/
task-2-box/ , Python, 1 linennunetv2/ training/ loss/ __init__.py - algo_submission/
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task-2-box/ , Python, 30 linesnnunetv2/ training/ loss/ deep_supervision.py - algo_submission/
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task-2-box/ , Python, 91 linesnnunetv2/ training/ loss/ focal_loss.py - algo_submission/
task-2-box/ , Python, 32 linesnnunetv2/ training/ loss/ robust_ce_loss.py - algo_submission/
task-2-box/ , Python, 1 linennunetv2/ training/ lr_scheduler/ __init__.py - algo_submission/
task-2-box/ , Python, 20 linesnnunetv2/ training/ lr_scheduler/ polylr.py - algo_submission/
task-2-box/ , Python, 1 linennunetv2/ training/ nnUNetTrainer/ __init__.py - algo_submission/
task-2-box/ , Python, 1,509 linesnnunetv2/ training/ nnUNetTrainer/ nnUNetTrainer.py - algo_submission/
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task-2-box/ , Python, 1 linennunetv2/ training/ nnUNetTrainer/ variants/ data_augmentation/ __init__.py - algo_submission/
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task-2-box/ , Python, 35 linesnnunetv2/ training/ nnUNetTrainer/ variants/ data_augmentation/ nnUNetTrainerNoDA.py - algo_submission/
task-2-box/ , Python, 28 linesnnunetv2/ training/ nnUNetTrainer/ variants/ data_augmentation/ nnUNetTrainerNoMirroring .py - algo_submission/
task-2-box/ , Python, 1 linennunetv2/ training/ nnUNetTrainer/ variants/ loss/ __init__.py - algo_submission/
task-2-box/ , Python, 41 linesnnunetv2/ training/ nnUNetTrainer/ variants/ loss/ nnUNetTrainerCELoss.py - algo_submission/
task-2-box/ , Python, 60 linesnnunetv2/ training/ nnUNetTrainer/ variants/ loss/ nnUNetTrainerDiceLoss.py - algo_submission/
task-2-box/ , Python, 457 linesnnunetv2/ training/ nnUNetTrainer/ variants/ loss/ nnUNetTrainerSkeletonRec all.py - algo_submission/
task-2-box/ , Python, 76 linesnnunetv2/ training/ nnUNetTrainer/ variants/ loss/ nnUNetTrainerTopkLoss.py - algo_submission/
task-2-box/ , Python, 1 linennunetv2/ training/ nnUNetTrainer/ variants/ lr_schedule/ __init__.py - algo_submission/
task-2-box/ , Python, 13 linesnnunetv2/ training/ nnUNetTrainer/ variants/ lr_schedule/ nnUNetTrainerCosAnneal.p y - algo_submission/
task-2-box/ , Python, 1 linennunetv2/ training/ nnUNetTrainer/ variants/ network_architecture/ __init__.py - algo_submission/
task-2-box/ , Python, 32 linesnnunetv2/ training/ nnUNetTrainer/ variants/ network_architecture/ nnUNetTrainerBN.py - algo_submission/
task-2-box/ , Python, 16 linesnnunetv2/ training/ nnUNetTrainer/ variants/ network_architecture/ nnUNetTrainerNoDeepSuper vision.py - algo_submission/
task-2-box/ , Python, 1 linennunetv2/ training/ nnUNetTrainer/ variants/ optimizer/ __init__.py - algo_submission/
task-2-box/ , Python, 58 linesnnunetv2/ training/ nnUNetTrainer/ variants/ optimizer/ nnUNetTrainerAdam.py - algo_submission/
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task-2-box/ , Python, 1 linennunetv2/ utilities/ __init__.py - algo_submission/
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task-2-box/ , Python, 74 linesnnunetv2/ utilities/ dataset_name_id_conversi on.py - algo_submission/
task-2-box/ , Python, 49 linesnnunetv2/ utilities/ ddp_allgather.py - algo_submission/
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task-2-box/ , Python, 123 linesnnunetv2/ utilities/ file_path_utilities.py - algo_submission/
task-2-box/ , Python, 24 linesnnunetv2/ utilities/ find_class_by_name.py - algo_submission/
task-2-box/ , Python, 43 linesnnunetv2/ utilities/ get_network_from_plans.p y - algo_submission/
task-2-box/ , Python, 27 linesnnunetv2/ utilities/ helpers.py - algo_submission/
task-2-box/ , Python, 60 linesnnunetv2/ utilities/ json_export.py - algo_submission/
task-2-box/ , Python, 1 linennunetv2/ utilities/ label_handling/ __init__.py - algo_submission/
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task-2-box/ , Python, 12 linesnnunetv2/ utilities/ network_initialization.p y - algo_submission/
task-2-box/ , Python, 275 linesnnunetv2/ utilities/ overlay_plots.py - algo_submission/
task-2-box/ , Python, 1 linennunetv2/ utilities/ plans_handling/ __init__.py - algo_submission/
task-2-box/ , Python, 339 linesnnunetv2/ utilities/ plans_handling/ plans_handler.py - algo_submission/
task-2-box/ , Python, 180 linesnnunetv2/ utilities/ sam.py - algo_submission/
task-2-box/ , Python, 69 linesnnunetv2/ utilities/ utils.py - algo_submission/
task-2-box/ , Shell, 38 linessave.sh - algo_submission/
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task-2-box/ , Python, 17 linestorch_utilities.py - algo_submission/
task-2-box/ , Python, 222 linesyour_algorithm.py - guides_topcow.ipynb, Jupyter, 605 lines
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documentation/ , Python, 1 line__init__.py - nnUNet/
nnunetv2/ , Python, 1 line__init__.py - nnUNet/
nnunetv2/ , Python, 1 linebatch_running/ __init__.py - nnUNet/
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nnunetv2/ , Python, 70 linesbatch_running/ benchmarking/ summarize_benchmark_resu lts.py - nnUNet/
nnunetv2/ , Python, 112 linesbatch_running/ collect_results_custom_D ecathlon.py - nnUNet/
nnunetv2/ , Python, 18 linesbatch_running/ collect_results_custom_D ecathlon_2d.py - nnUNet/
nnunetv2/ , Python, 105 linesbatch_running/ generate_lsf_runs_custom Decathlon.py - nnUNet/
nnunetv2/ , Python, 1 linebatch_running/ release_trainings/ __init__.py - nnUNet/
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nnunetv2/ , Python, 93 linesbatch_running/ release_trainings/ nnunetv2_v1/ generate_lsf_commands.py - nnUNet/
nnunetv2/ , Python, 10 linesconfiguration.py - nnUNet/
nnunetv2/ , Python, 114 linesdataset_conversion/ Dataset027_ACDC.py - nnUNet/
nnunetv2/ , Python, 110 linesdataset_conversion/ Dataset042_BraTS18.py - nnUNet/
nnunetv2/ , Python, 110 linesdataset_conversion/ Dataset043_BraTS19.py - nnUNet/
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nnunetv2/ , Python, 198 linesdataset_conversion/ Dataset114_MNMs.py - nnUNet/
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nnunetv2/ , Python, 87 linesdataset_conversion/ Dataset120_RoadSegmentat ion.py - nnUNet/
nnunetv2/ , Python, 98 linesdataset_conversion/ Dataset137_BraTS21.py - nnUNet/
nnunetv2/ , Python, 70 linesdataset_conversion/ Dataset218_Amos2022_task 1.py - nnUNet/
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nnunetv2/ , Python, 50 linesdataset_conversion/ Dataset220_KiTS2023.py - nnUNet/
nnunetv2/ , Python, 70 linesdataset_conversion/ Dataset221_AutoPETII_202 3.py - nnUNet/
nnunetv2/ , Python, 59 linesdataset_conversion/ Dataset223_AMOS2022postC hallenge.py - nnUNet/
nnunetv2/ , Python, 32 linesdataset_conversion/ Dataset988_dummyDataset4 .py - nnUNet/
nnunetv2/ , Python, 1 linedataset_conversion/ __init__.py - nnUNet/
nnunetv2/ , Python, 132 linesdataset_conversion/ convert_MSD_dataset.py - nnUNet/
nnunetv2/ , Python, 53 linesdataset_conversion/ convert_raw_dataset_from _old_nnunet_format.py - nnUNet/
nnunetv2/ , Python, 75 linesdataset_conversion/ datasets_for_integration _tests/ Dataset996_IntegrationTe st_Hippocampus_regions_i gnore.py - nnUNet/
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nnunetv2/ , Python, 1 linedataset_conversion/ datasets_for_integration _tests/ __init__.py - nnUNet/
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nnunetv2/ , Python, 1 lineensembling/ __init__.py - nnUNet/
nnunetv2/ , Python, 206 linesensembling/ ensemble.py - nnUNet/
nnunetv2/ , Python, 1 lineevaluation/ __init__.py - nnUNet/
nnunetv2/ , Python, 58 linesevaluation/ accumulate_cv_results.py - nnUNet/
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Tracing map
Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.
What the map holds:
- 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
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- 2 matches between paragraphs of the paper and lines of the code (method lexical-v1);
- neither the text of the paper nor the code itself.
Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
No dataset and no data link were found in the paper.
Data Availability
The in-house dataset used for developing of the algorithm in the current study is not publicly available due to the confidentiality policy and institutional patient privacy regulation. The CODEC-IV dataset can be obtained in accordance with the original data provider’s and license terms.
Reproduced under the paper's license (CC BY), from the paper cited above.
Versions
The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.
Version 3, 28 September 2026
- Publisher: n/a → Springer Science+Business Media
- Funding: added Nvidia; Universitat de Girona: IFUdG2024; Ministerio de Ciencia, Innovación y Universidades: PID2023, PID2023-146187OB-I00, PRE2021-099121, DPI2020-114769RB-I00; Institució Catalana de Recerca i Estudis Avançats; Education, Audiovisual and Culture Executive Agency
Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 9 authors, 4 keywords, 5 MeSH terms, 30 references.
Cite
This paper
Abramova, V., Oliver, A., Lal-Trehan Estrada, U. M., Hamadache, R. E., Martínez Arias, P., Freixenet, J., Terceño, M., Silva, Y., & Lladó, X. (2026). Circle of Willis-Guided Localization for Simultaneous Detection and Classification of Large Vessel Occlusions in Brain CTA. Neuroinformatics, 24(4), 62. https://
BibTeX
@article{abramova2026cir
author = {Abramova, Valeriia and Oliver, Arnau and Lal-Trehan Estrada, Uma M and Hamadache, Rachika E and Martínez Arias, Paola and Freixenet, Jordi and Terceño, Mikel and Silva, Yolanda and Lladó, Xavier},
title = {{Circle of Willis-Guided Localization for Simultaneous Detection and Classification of Large Vessel Occlusions in Brain CTA}},
journal = {Neuroinformatics},
year = {2026},
month = sep,
volume = {24},
number = {4},
pages = {62},
publisher = {Springer Science+Business Media},
issn = {1539-2791},
doi = {10.1007/
url = {https://
pmid = {42747736},
pmcid = {PMC13582341}
}
RIS
TY - JOUR
AU - Abramova, Valeriia
AU - Oliver, Arnau
AU - Lal-Trehan Estrada, Uma M
AU - Hamadache, Rachika E
AU - Martínez Arias, Paola
AU - Freixenet, Jordi
AU - Terceño, Mikel
AU - Silva, Yolanda
AU - Lladó, Xavier
TI - Circle of Willis-Guided Localization for Simultaneous Detection and Classification of Large Vessel Occlusions in Brain CTA
T2 - Neuroinformatics
J2 - Neuroinformatics
PY - 2026
DA - 2026/
VL - 24
IS - 4
SP - 62
SN - 1539-2791
PB - Springer Science+Business Media
DO - 10.1007/
UR - https://
LA - en
ER -
CSL-JSON
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