论文标题

培训通用实例分割网络,以了解各种细胞类型和成像方式的活细胞图像

Training a universal instance segmentation network for live cell images of various cell types and imaging modalities

论文作者

Guo, Tianqi, Wang, Yin, Solorio, Luis, Allebach, Jan P.

论文摘要

我们分享了我们最近的发现,以试图培训通用分割网络的各种细胞类型和成像方式。我们的方法建立在广义的U-NET体系结构上,该体系结构允许单独评估每个组件。我们修改了传统的二进制培训目标,以包括三个直接实例细分的类。进行了有关培训方案,培训设置,网络骨架和各个模块的详细实验。我们提出的培训方案依次从每个数据集中汲取小匹配,并且在优化步骤之前积累了梯度。我们发现,培训通用网络的关键是所有数据集上的历史监督,并且有必要以公正的方式对每个数据集进行采样。我们的实验还表明,可能存在共同的特征来定义细胞类型和成像方式的细胞边界,这可以使训练有素的模型完全看不见数据集。一些培训技巧可以进一步提高细分性能,包括交叉渗透损失功能中的班级权重,精心设计的学习率调度程序,更大的图像作物以进行上下文信息,以及不平衡的类别的其他损失条款。我们还发现,由于它们更可靠的统计估计和更高的语义理解,分割性能可以受益于组规范化层和ARTOUS空间金字塔池模块。我们使用其中一种已发达的变体参加了在IEEE国际生物医学成像(ISBI)2021举行的第六个细胞跟踪挑战(CTC)。我们的方法被评估为在主要曲目的初始提交期间,作为最佳跑步者,并在额外的竞争中获得了第三名,以准备摘要出版物。

We share our recent findings in an attempt to train a universal segmentation network for various cell types and imaging modalities. Our method was built on the generalized U-Net architecture, which allows the evaluation of each component individually. We modified the traditional binary training targets to include three classes for direct instance segmentation. Detailed experiments were performed regarding training schemes, training settings, network backbones, and individual modules on the segmentation performance. Our proposed training scheme draws minibatches in turn from each dataset, and the gradients are accumulated before an optimization step. We found that the key to training a universal network is all-time supervision on all datasets, and it is necessary to sample each dataset in an unbiased way. Our experiments also suggest that there might exist common features to define cell boundaries across cell types and imaging modalities, which could allow application of trained models to totally unseen datasets. A few training tricks can further boost the segmentation performance, including uneven class weights in the cross-entropy loss function, well-designed learning rate scheduler, larger image crops for contextual information, and additional loss terms for unbalanced classes. We also found that segmentation performance can benefit from group normalization layer and Atrous Spatial Pyramid Pooling module, thanks to their more reliable statistics estimation and improved semantic understanding, respectively. We participated in the 6th Cell Tracking Challenge (CTC) held at IEEE International Symposium on Biomedical Imaging (ISBI) 2021 using one of the developed variants. Our method was evaluated as the best runner up during the initial submission for the primary track, and also secured the 3rd place in an additional round of competition in preparation for the summary publication.

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