Junxiao Chen, Ruixue Wang, Wei Dong, Hua He, Shiyong Wang
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The decoder employs a dual-mechanism architecture: The first branch of the mechanism splits into two parallel paths for nuclear segmentation, producing nuclear pixel (NP) and horizontal and vertical distance (HV) predictions, while the second mechanism branch focuses on type prediction (TP). The NP and HV branches leverage densely connected blocks to facilitate layer-by-layer feature transmission and reuse, while the TP branch employs channel attention to adaptively focus on critical features. Comprehensive data augmentation including morphology-preserving geometric transformations and adaptive H&E channel adjustments was applied. To address class imbalance, type-aware sampling was applied. The model was evaluated on public tissue image datasets including CONSEP, PanNuke, CPM17, and KUMAR. The performance in nuclear segmentation was evaluated using the Dice Similarity Coefficient (DICE), the Aggregated Jaccard Index (AJI) and Panoptic Quality (PQ), and the classification performance was evaluated using F1 scores and category-specific F1 scores. In addition, computational complexity, measured in Giga Floating Point Operations Per Second (GFLOPS), was used as an indicator of resource consumption.</p><p><strong>Results: </strong>HistoNeXt demonstrated competitive performance across multiple datasets: achieving a DICE score of 0.874, an AJI of 0.722, and a PQ of 0.689 on the CPM17 dataset; a DICE score of 0.826, an AJI of 0.625, and a PQ of 0.565 on KUMAR; and performance comparable to Transformer-based models, such as CellViT-SAM-H, on PanNuke, with a binary PQ of 0.6794, a multi-class PQ of 0.4940, and an overall F1 score of 0.82. On the CONSEP dataset, it achieved a DICE score of 0.843, an AJI of 0.592, a PQ of 0.532, and an overall classification F1 score of 0.773. Specific F1 scores for various cell types were as follows: 0.653 for malignant or dysplastic epithelial cells, 0.516 for normal epithelial cells, 0.659 for inflammatory cells, and 0.587 for spindle cells. The tiny model's complexity was 33.7 GFLOPS.</p><p><strong>Conclusion: </strong>By integrating novel convolutional technology and employing a pyramid fusion of dual-mechanism characteristics, HistoNeXt enhances both the precision and efficiency of nuclear segmentation and classification. Its low computational complexity makes the model well suited for local deployment in resource-constrained environments, thereby supporting a broad spectrum of clinical and research applications. This represents a significant advance in the application of convolutional neural networks in digital pathology analysis.</p>","PeriodicalId":9020,"journal":{"name":"BMC Medical Imaging","volume":"25 1","pages":"9"},"PeriodicalIF":2.9000,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11706021/pdf/","citationCount":"0","resultStr":"{\"title\":\"HistoNeXt: dual-mechanism feature pyramid network for cell nuclear segmentation and classification.\",\"authors\":\"Junxiao Chen, Ruixue Wang, Wei Dong, Hua He, Shiyong Wang\",\"doi\":\"10.1186/s12880-025-01550-2\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Purpose: </strong>To develop an end-to-end convolutional neural network model for analyzing hematoxylin and eosin(H&E)-stained histological images, enhancing the performance and efficiency of nuclear segmentation and classification within the digital pathology workflow.</p><p><strong>Methods: </strong>We propose a dual-mechanism feature pyramid fusion technique that integrates nuclear segmentation and classification tasks to construct the HistoNeXt network model. HistoNeXt utilizes an encoder-decoder architecture, where the encoder, based on the advanced ConvNeXt convolutional framework, efficiently and accurately extracts multi-level abstract features from tissue images. These features are subsequently shared with the decoder. The decoder employs a dual-mechanism architecture: The first branch of the mechanism splits into two parallel paths for nuclear segmentation, producing nuclear pixel (NP) and horizontal and vertical distance (HV) predictions, while the second mechanism branch focuses on type prediction (TP). The NP and HV branches leverage densely connected blocks to facilitate layer-by-layer feature transmission and reuse, while the TP branch employs channel attention to adaptively focus on critical features. Comprehensive data augmentation including morphology-preserving geometric transformations and adaptive H&E channel adjustments was applied. To address class imbalance, type-aware sampling was applied. The model was evaluated on public tissue image datasets including CONSEP, PanNuke, CPM17, and KUMAR. The performance in nuclear segmentation was evaluated using the Dice Similarity Coefficient (DICE), the Aggregated Jaccard Index (AJI) and Panoptic Quality (PQ), and the classification performance was evaluated using F1 scores and category-specific F1 scores. In addition, computational complexity, measured in Giga Floating Point Operations Per Second (GFLOPS), was used as an indicator of resource consumption.</p><p><strong>Results: </strong>HistoNeXt demonstrated competitive performance across multiple datasets: achieving a DICE score of 0.874, an AJI of 0.722, and a PQ of 0.689 on the CPM17 dataset; a DICE score of 0.826, an AJI of 0.625, and a PQ of 0.565 on KUMAR; and performance comparable to Transformer-based models, such as CellViT-SAM-H, on PanNuke, with a binary PQ of 0.6794, a multi-class PQ of 0.4940, and an overall F1 score of 0.82. 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引用次数: 0
摘要
目的:建立一个端到端的卷积神经网络模型,用于分析苏木精和伊红(H&E)染色的组织图像,提高数字病理工作流程中核分割和分类的性能和效率。方法:提出一种融合核分割和分类任务的双机制特征金字塔融合技术,构建HistoNeXt网络模型。HistoNeXt采用编码器-解码器架构,其中编码器基于先进的ConvNeXt卷积框架,有效准确地从组织图像中提取多级抽象特征。这些特征随后与解码器共享。解码器采用双机制架构:机制的第一个分支分为两条并行路径进行核分割,产生核像素(NP)和水平和垂直距离(HV)预测,而机制的第二个分支则专注于类型预测(TP)。NP和HV分支利用密集连接的块来促进逐层特征的传输和重用,而TP分支利用通道关注来自适应地关注关键特征。综合数据增强包括形态保持几何变换和自适应H&E通道调整。为了解决类不平衡问题,采用了类型感知抽样。该模型在包括CONSEP、PanNuke、CPM17和KUMAR在内的公共组织图像数据集上进行评估。采用Dice Similarity Coefficient (Dice)、aggregate Jaccard Index (AJI)和Panoptic Quality (PQ)对核分割性能进行评价,采用F1分数和类别特异性F1分数对分类性能进行评价。此外,计算复杂性(以每秒千兆浮点操作数(GFLOPS)衡量)被用作资源消耗的指标。结果:HistoNeXt在多个数据集上表现出具有竞争力的性能:在CPM17数据集上,DICE得分为0.874,AJI为0.722,PQ为0.689;KUMAR的DICE得分为0.826,AJI为0.625,PQ为0.565;性能可与PanNuke上基于transformer的模型(如cellviti - sam - h)相媲美,二进制PQ为0.6794,多类PQ为0.4940,F1总分为0.82。在CONSEP数据集上,其DICE得分为0.843,AJI得分为0.592,PQ得分为0.532,总体分类F1得分为0.773。不同细胞类型的特异性F1评分如下:恶性或发育不良上皮细胞为0.653,正常上皮细胞为0.516,炎症细胞为0.659,梭形细胞为0.587。这个微型模型的复杂度为33.7 GFLOPS。结论:HistoNeXt通过融合新的卷积技术和双机制特征的金字塔融合,提高了核分割和分类的精度和效率。其较低的计算复杂度使该模型非常适合在资源受限的环境中进行本地部署,从而支持广泛的临床和研究应用。这代表了卷积神经网络在数字病理分析中的应用取得了重大进展。
HistoNeXt: dual-mechanism feature pyramid network for cell nuclear segmentation and classification.
Purpose: To develop an end-to-end convolutional neural network model for analyzing hematoxylin and eosin(H&E)-stained histological images, enhancing the performance and efficiency of nuclear segmentation and classification within the digital pathology workflow.
Methods: We propose a dual-mechanism feature pyramid fusion technique that integrates nuclear segmentation and classification tasks to construct the HistoNeXt network model. HistoNeXt utilizes an encoder-decoder architecture, where the encoder, based on the advanced ConvNeXt convolutional framework, efficiently and accurately extracts multi-level abstract features from tissue images. These features are subsequently shared with the decoder. The decoder employs a dual-mechanism architecture: The first branch of the mechanism splits into two parallel paths for nuclear segmentation, producing nuclear pixel (NP) and horizontal and vertical distance (HV) predictions, while the second mechanism branch focuses on type prediction (TP). The NP and HV branches leverage densely connected blocks to facilitate layer-by-layer feature transmission and reuse, while the TP branch employs channel attention to adaptively focus on critical features. Comprehensive data augmentation including morphology-preserving geometric transformations and adaptive H&E channel adjustments was applied. To address class imbalance, type-aware sampling was applied. The model was evaluated on public tissue image datasets including CONSEP, PanNuke, CPM17, and KUMAR. The performance in nuclear segmentation was evaluated using the Dice Similarity Coefficient (DICE), the Aggregated Jaccard Index (AJI) and Panoptic Quality (PQ), and the classification performance was evaluated using F1 scores and category-specific F1 scores. In addition, computational complexity, measured in Giga Floating Point Operations Per Second (GFLOPS), was used as an indicator of resource consumption.
Results: HistoNeXt demonstrated competitive performance across multiple datasets: achieving a DICE score of 0.874, an AJI of 0.722, and a PQ of 0.689 on the CPM17 dataset; a DICE score of 0.826, an AJI of 0.625, and a PQ of 0.565 on KUMAR; and performance comparable to Transformer-based models, such as CellViT-SAM-H, on PanNuke, with a binary PQ of 0.6794, a multi-class PQ of 0.4940, and an overall F1 score of 0.82. On the CONSEP dataset, it achieved a DICE score of 0.843, an AJI of 0.592, a PQ of 0.532, and an overall classification F1 score of 0.773. Specific F1 scores for various cell types were as follows: 0.653 for malignant or dysplastic epithelial cells, 0.516 for normal epithelial cells, 0.659 for inflammatory cells, and 0.587 for spindle cells. The tiny model's complexity was 33.7 GFLOPS.
Conclusion: By integrating novel convolutional technology and employing a pyramid fusion of dual-mechanism characteristics, HistoNeXt enhances both the precision and efficiency of nuclear segmentation and classification. Its low computational complexity makes the model well suited for local deployment in resource-constrained environments, thereby supporting a broad spectrum of clinical and research applications. This represents a significant advance in the application of convolutional neural networks in digital pathology analysis.
期刊介绍:
BMC Medical Imaging is an open access journal publishing original peer-reviewed research articles in the development, evaluation, and use of imaging techniques and image processing tools to diagnose and manage disease.