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Open problems in Image segmentation

Lack of whole-slide image generation for histopathology1 paper raises it · 1 addresses it
Current generative models only produce small patches, but clinical labels and reports operate at the whole-slide level, limiting alignment with real-world supervision.
- BigCell: Generating Gigapixel Whole-Slide Imagesraises · addresses
Limited longitudinal multimodal reasoning benchmarks1 paper raises it · 1 addresses it
Most medical benchmarks assess reasoning over preselected evidence, not the ability to seek and integrate evidence across longitudinal clinical records and imaging.
- From Given to Gathered Evidence: Agentic Learning for Longitudinal Medical Reasoningraises · addresses
Frozen models cannot learn from deployment experience1 paper raises it · 1 addresses it
Deployed models in medicine do not adapt to new clinical evidence or updated guidelines without retraining, which is often impractical.
- Frozen Models, Evolving Expertise: Model-Agnostic Learning from Deployment Experience for Multimodal Medical AIraises · addresses
Benchmark misalignment with real-world clinical use1 paper raises it · 1 addresses it
Public benchmarks often do not reflect the tasks, intents, or constraints of actual clinician queries, reducing their predictive value for deployment performance.
- Clinician use of language models diverges from how the models are evaluatedraises · addresses
Sensitivity to incidental information in clinical reasoning1 paper raises it · 1 addresses it
Models may incorporate or misattribute irrelevant details (e.g., small talk, background noise) in clinical documentation or reasoning, risking contamination.
- Large language models are vulnerable to incidental information in clinical documentation and reasoningraises · addresses

Named by an AI from these papers' abstracts.

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Topics in this field

image segmentation · volumetric · medical image403 papers61 this week
radiology report generation · medical vision language · vision language models127 papers38 this week
clinical reasoning · question answering · language models205 papers37 this week
patient history · clinical data · health records109 papers26 this week
eeg foundation models · electroencephalography eeg · eeg foundation155 papers24 this week
electrocardiogram ecg · electrocardiogram · ecgs145 papers17 this week

Topics in this field

Active contributors · 90 days

Active contributors

Activity · 12 weeks

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All papers in Research

arXiv cs.LGOct 2
ZeroMAG: Zero-Shot Multimodal Adapter Generation for Plug-and-Play EEG Foundation Models
Yubo Wang, Jingying Ma, Xinliang Zhou, Yangxuan Zhou, Jiquan Wang +6
EEG foundation models (EFMs) capture reusable knowledge from large-scale EEG data, while many EEG recordings also include companion physiological signals that provide complementary information beyond the EEG-only interface. The challenge is to preserve this pretrained knowledge while extending the EFM to heterogeneous multimodal recordings through an adaptation inferred from unlabeled target data. We introduce ZeroMAG, a zero-shot multimodal adapter generation framework that extends a frozen EEG encoder and prediction head using unlabeled target recordings, without target labels or target-side optimization. The target datasets are held out from all model training and selection in the ZeroMAG pipeline. ZeroMAG organizes companion modalities around a configuration-invariant adapter, constructs a modality-subject-task condition from unlabeled recordings and task context, and generates adapter weights in a function-constrained latent space learned from source adapters. Across six held-out target datasets and three EFM backbones, ZeroMAG improves balanced accuracy by 7.22 percentage points over EEG-only inference and 4.89 points over direct weight regression, while coming within 0.50…
PDF arXiv
arXiv eess.IVOct 2
Abdominal Ultrasound Simulation from Semantic Labels using Paired Label-to-Physics-Based Image Translation
Santiago Vitale, Duilio Deangeli, Ignacio Larrabide, José Ignacio Orlando
Purpose: Current abdominal ultrasound (US) simulation methods often require CT-based anatomical references for ray-casting, limiting deformation and pathology variability. We propose a learning-based pipeline trained to predict physics-based images derived from CT scans from semantic labels, enabling controlled simulations without patient-specific CT volumes at inference time. Methods: We introduce a two-stage pipeline that maps anatomical segmentations to realistic US images through a simplified US image. Stage~I synthesizes this image from semantic labels using models trained on CT-based ray-casting outputs. Stage~II refines it into a realistic US scan using anatomically guided unpaired translation. Deformations and pathologies are generated by editing anatomical maps. Results: We evaluated Pix2Pix and the Semantic Diffusion Model (SDM) in Stage~I, followed by segmentation-guided CycleGAN (SG-CycleGAN) refinement in Stage~II. SDM significantly outperformed Pix2Pix in morphological metrics, including MAE (19.85 vs. 21.65), SSIM (0.28 vs. 0.24), and mIoU (0.43 vs. 0.29), whereas Pix2Pix yielded better perceptual point estimates (LPIPS: 0.17 vs. 0.19; FID: 0.32 vs. 0.37; KID: 0.25…
PDF arXiv
arXiv cs.CVOct 2
Fed-ADApt: Federated Anytime Depth Adaptation for Resource-Aware Medical Image Segmentation
Abhijeet Parida, Zhifan Jiang, Pooneh Roshanitabrizi, Austin Tapp, Maria J. Ledesma-Carbayo +4
Federated learning (FL) enables collaborative training of medical image segmentation models without sharing raw patient data, yet existing approaches assume a homogeneous compute budget across institutions, limiting participation of low-resource sites. We propose Fed-ADApt, a depth-adaptive federated framework for UNet-based segmentation that jointly addresses low-compute training and inference. Fed-ADApt integrates multi-depth supervision with hierarchical depth-wise aggregation, allowing each site to train according to its local compute budget while contributing to a global model that supports dynamic depth selection at deployment. We evaluated Fed-ADApt on multi-site 2D retinal fundus disc segmentation and 3D brain tumor segmentation. Across both tasks, federated collaboration substantially improves robustness under domain shift. Fed-ADApt matched the full-resource FedAvg performance in 3D and achieved competitive 2D performance with a 4.7% average Dice reduction, while reducing average inference cost by 19.5% in 3D and 34.5% in 2D and substantially reducing training cost by 98% at the most constrained sites. Importantly, Fed-ADApt enables low-resource institutions that cannot…
PDF arXiv
arXiv cs.CVOct 2
Preserving Anatomical Continuity: Three-Stage Pipeline for Colon Segmentation in 3D Abdominal CT Scans
Deshan Kalupahana, Sonit Singh, Praveen Ravindran, Arcot Sowmya
Accurate colon segmentation from CT images is essential for colorectal disease analysis, yet deep learning based methods often produce disconnected predictions due to complex anatomy. This study introduces a three-stage, topology-preserving segmentation pipeline to address this issue. The first stage performs initial deep learning-based segmentation, followed by centreline bridging to reconnect disjoint regions and a reconstruction stage to refine continuity. Evaluations on TotalSegmentator and RAOS datasets using overlap, distance and topology-based metrics demonstrate improved structural consistency while maintaining segmentation accuracy. The proposed method enhances topological integrity, enabling more reliable colon segmentation for clinical and research applications.
PDF arXiv
arXiv q-bio.NCOct 2
Contrastive Neural Embeddings Reveal Individual Traits Beyond Conversational Role
Hubert Huang, Michelle McCleod, Brendan Ames, Evie Malaia
Contrastive representation learning is increasingly used to recover low-dimensional structure from neural recordings, but its output is typically validated by decoding accuracy rather than by the geometry of the manifold it produces. We apply CEBRA to EEG recorded from dyads in conversation, and analyze the resulting embedding, which training constrains to the 2D sphere. Labels describing the dyads, including the absolute difference between partners' autism-quotient scores, decode well above chance (0.77 against a 0.55 majority baseline for binary AQ magnitude; 0.44 against 0.25 for the six-class $|Δ$AQ$|$ partition). However, the two permutation controls have notable differences in results: permuting labels over a frozen embedding yields p = 0.001, whereas retraining the encoder under each permutation yields p = 0.50. Only the latter tests the label rather than the geometry. Consistent with this, spherical mixture structure and per-class dispersion track identity rather than autism trait differences in dyads; frequency-band and non-oscillatory activity ablation controls do not change the results. However, participant-level model does separate from its identity-aware null (p =…
PDF arXiv
arXiv cs.CVOct 2
A Fully Automatic Pipeline for 3D Dendrite Instance Segmentation in SBF-SEM
Zewen Zhuo, Ilya Belevich, Eija Jokitalo, Alejandra Sierra, Jussi Tohka
Accurate three-dimensional (3D) reconstruction of individual dendrites in serial block-face scanning electron microscopy (SBF-SEM) is essential for quantifying structural plasticity in the brain, yet manual annotation at scale is infeasible. We present a fully automatic pipeline for 3D dendrite instance segmentation that unifies YOLOv6-guided Segment Anything Model (SAM) prompting on downsampled slices, iterative two-dimensional mask refinement, random forest 3D instance linking, and instance-aware high-resolution refinement using nnU-Net at native resolution into a single system requiring no manual prompting at inference. Applied to hippocampal CA1 SBF-SEM datasets from a control rat and a pilocarpine- induced epileptic rat, our pipeline reconstructs coherent, well- separated dendrites with high semantic accuracy (Dice 0.93 and 0.91) and strong instance-level performance on control tissue, while analysis of the more challenging epileptic tissue identifies instance recognition in dense regions as the principal remaining limitation. The high-resolution refinement stage recovers thin dendritic protrusions, providing a basis for downstream spine- level analysis. Code is available at…
PDF arXiv

Papers

Topics in this field

image segmentation · volumetric · medical image403 papers61 this week
radiology report generation · medical vision language · vision language models127 papers38 this week
clinical reasoning · question answering · language models205 papers37 this week
patient history · clinical data · health records109 papers26 this week
eeg foundation models · electroencephalography eeg · eeg foundation155 papers24 this week
electrocardiogram ecg · electrocardiogram · ecgs145 papers17 this week

Active contributors · 90 days

Activity · 12 weeks

Recent papers

All papers in Research

arXiv cs.LGOct 2
ZeroMAG: Zero-Shot Multimodal Adapter Generation for Plug-and-Play EEG Foundation Models
Yubo Wang, Jingying Ma, Xinliang Zhou, Yangxuan Zhou, Jiquan Wang +6
EEG foundation models (EFMs) capture reusable knowledge from large-scale EEG data, while many EEG recordings also include companion physiological signals that provide complementary information beyond the EEG-only interface. The challenge is to preserve this pretrained knowledge while extending the EFM to heterogeneous multimodal recordings through an adaptation inferred from unlabeled target data. We introduce ZeroMAG, a zero-shot multimodal adapter generation framework that extends a frozen EEG encoder and prediction head using unlabeled target recordings, without target labels or target-side optimization. The target datasets are held out from all model training and selection in the ZeroMAG pipeline. ZeroMAG organizes companion modalities around a configuration-invariant adapter, constructs a modality-subject-task condition from unlabeled recordings and task context, and generates adapter weights in a function-constrained latent space learned from source adapters. Across six held-out target datasets and three EFM backbones, ZeroMAG improves balanced accuracy by 7.22 percentage points over EEG-only inference and 4.89 points over direct weight regression, while coming within 0.50…
PDF arXiv
arXiv eess.IVOct 2
Abdominal Ultrasound Simulation from Semantic Labels using Paired Label-to-Physics-Based Image Translation
Santiago Vitale, Duilio Deangeli, Ignacio Larrabide, José Ignacio Orlando
Purpose: Current abdominal ultrasound (US) simulation methods often require CT-based anatomical references for ray-casting, limiting deformation and pathology variability. We propose a learning-based pipeline trained to predict physics-based images derived from CT scans from semantic labels, enabling controlled simulations without patient-specific CT volumes at inference time. Methods: We introduce a two-stage pipeline that maps anatomical segmentations to realistic US images through a simplified US image. Stage~I synthesizes this image from semantic labels using models trained on CT-based ray-casting outputs. Stage~II refines it into a realistic US scan using anatomically guided unpaired translation. Deformations and pathologies are generated by editing anatomical maps. Results: We evaluated Pix2Pix and the Semantic Diffusion Model (SDM) in Stage~I, followed by segmentation-guided CycleGAN (SG-CycleGAN) refinement in Stage~II. SDM significantly outperformed Pix2Pix in morphological metrics, including MAE (19.85 vs. 21.65), SSIM (0.28 vs. 0.24), and mIoU (0.43 vs. 0.29), whereas Pix2Pix yielded better perceptual point estimates (LPIPS: 0.17 vs. 0.19; FID: 0.32 vs. 0.37; KID: 0.25…
PDF arXiv
arXiv cs.CVOct 2
Fed-ADApt: Federated Anytime Depth Adaptation for Resource-Aware Medical Image Segmentation
Abhijeet Parida, Zhifan Jiang, Pooneh Roshanitabrizi, Austin Tapp, Maria J. Ledesma-Carbayo +4
Federated learning (FL) enables collaborative training of medical image segmentation models without sharing raw patient data, yet existing approaches assume a homogeneous compute budget across institutions, limiting participation of low-resource sites. We propose Fed-ADApt, a depth-adaptive federated framework for UNet-based segmentation that jointly addresses low-compute training and inference. Fed-ADApt integrates multi-depth supervision with hierarchical depth-wise aggregation, allowing each site to train according to its local compute budget while contributing to a global model that supports dynamic depth selection at deployment. We evaluated Fed-ADApt on multi-site 2D retinal fundus disc segmentation and 3D brain tumor segmentation. Across both tasks, federated collaboration substantially improves robustness under domain shift. Fed-ADApt matched the full-resource FedAvg performance in 3D and achieved competitive 2D performance with a 4.7% average Dice reduction, while reducing average inference cost by 19.5% in 3D and 34.5% in 2D and substantially reducing training cost by 98% at the most constrained sites. Importantly, Fed-ADApt enables low-resource institutions that cannot…
PDF arXiv
arXiv cs.CVOct 2
Preserving Anatomical Continuity: Three-Stage Pipeline for Colon Segmentation in 3D Abdominal CT Scans
Deshan Kalupahana, Sonit Singh, Praveen Ravindran, Arcot Sowmya
Accurate colon segmentation from CT images is essential for colorectal disease analysis, yet deep learning based methods often produce disconnected predictions due to complex anatomy. This study introduces a three-stage, topology-preserving segmentation pipeline to address this issue. The first stage performs initial deep learning-based segmentation, followed by centreline bridging to reconnect disjoint regions and a reconstruction stage to refine continuity. Evaluations on TotalSegmentator and RAOS datasets using overlap, distance and topology-based metrics demonstrate improved structural consistency while maintaining segmentation accuracy. The proposed method enhances topological integrity, enabling more reliable colon segmentation for clinical and research applications.
PDF arXiv
arXiv q-bio.NCOct 2
Contrastive Neural Embeddings Reveal Individual Traits Beyond Conversational Role
Hubert Huang, Michelle McCleod, Brendan Ames, Evie Malaia
Contrastive representation learning is increasingly used to recover low-dimensional structure from neural recordings, but its output is typically validated by decoding accuracy rather than by the geometry of the manifold it produces. We apply CEBRA to EEG recorded from dyads in conversation, and analyze the resulting embedding, which training constrains to the 2D sphere. Labels describing the dyads, including the absolute difference between partners' autism-quotient scores, decode well above chance (0.77 against a 0.55 majority baseline for binary AQ magnitude; 0.44 against 0.25 for the six-class $|Δ$AQ$|$ partition). However, the two permutation controls have notable differences in results: permuting labels over a frozen embedding yields p = 0.001, whereas retraining the encoder under each permutation yields p = 0.50. Only the latter tests the label rather than the geometry. Consistent with this, spherical mixture structure and per-class dispersion track identity rather than autism trait differences in dyads; frequency-band and non-oscillatory activity ablation controls do not change the results. However, participant-level model does separate from its identity-aware null (p =…
PDF arXiv
arXiv cs.CVOct 2
A Fully Automatic Pipeline for 3D Dendrite Instance Segmentation in SBF-SEM
Zewen Zhuo, Ilya Belevich, Eija Jokitalo, Alejandra Sierra, Jussi Tohka
Accurate three-dimensional (3D) reconstruction of individual dendrites in serial block-face scanning electron microscopy (SBF-SEM) is essential for quantifying structural plasticity in the brain, yet manual annotation at scale is infeasible. We present a fully automatic pipeline for 3D dendrite instance segmentation that unifies YOLOv6-guided Segment Anything Model (SAM) prompting on downsampled slices, iterative two-dimensional mask refinement, random forest 3D instance linking, and instance-aware high-resolution refinement using nnU-Net at native resolution into a single system requiring no manual prompting at inference. Applied to hippocampal CA1 SBF-SEM datasets from a control rat and a pilocarpine- induced epileptic rat, our pipeline reconstructs coherent, well- separated dendrites with high semantic accuracy (Dice 0.93 and 0.91) and strong instance-level performance on control tissue, while analysis of the more challenging epileptic tissue identifies instance recognition in dense regions as the principal remaining limitation. The high-resolution refinement stage recovers thin dendritic protrusions, providing a basis for downstream spine- level analysis. Code is available at…
PDF arXiv

Open problems in Image segmentation

Lack of whole-slide image generation for histopathology1 paper raises it · 1 addresses it
Current generative models only produce small patches, but clinical labels and reports operate at the whole-slide level, limiting alignment with real-world supervision.
- BigCell: Generating Gigapixel Whole-Slide Imagesraises · addresses
Limited longitudinal multimodal reasoning benchmarks1 paper raises it · 1 addresses it
Most medical benchmarks assess reasoning over preselected evidence, not the ability to seek and integrate evidence across longitudinal clinical records and imaging.
- From Given to Gathered Evidence: Agentic Learning for Longitudinal Medical Reasoningraises · addresses
Frozen models cannot learn from deployment experience1 paper raises it · 1 addresses it
Deployed models in medicine do not adapt to new clinical evidence or updated guidelines without retraining, which is often impractical.
- Frozen Models, Evolving Expertise: Model-Agnostic Learning from Deployment Experience for Multimodal Medical AIraises · addresses
Benchmark misalignment with real-world clinical use1 paper raises it · 1 addresses it
Public benchmarks often do not reflect the tasks, intents, or constraints of actual clinician queries, reducing their predictive value for deployment performance.
- Clinician use of language models diverges from how the models are evaluatedraises · addresses
Sensitivity to incidental information in clinical reasoning1 paper raises it · 1 addresses it
Models may incorporate or misattribute irrelevant details (e.g., small talk, background noise) in clinical documentation or reasoning, risking contamination.
- Large language models are vulnerable to incidental information in clinical documentation and reasoningraises · addresses

Named by an AI from these papers' abstracts.

Fields · AI · updated 1h ago

Image segmentation

Found by the topic model: image segmentation, clinical reasoning, eeg foundation models.

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