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首页> 外文期刊>Journal of Structural Biology >JUST (Java User Segmentation Tool) for semi-automatic segmentation of tomographic maps.
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JUST (Java User Segmentation Tool) for semi-automatic segmentation of tomographic maps.

机译：JUST（Java用户细分工具），用于断层图的半自动细分。

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We are presenting a program for interactive segmentation of tomographic maps, based on objective criteria so as to yield reproducible results. The strategy starts with the automatic segmentation of the entire volume with the watershed algorithm in 3D. The watershed regions are clustered successively by supervised classification, allowing the segmentation of known organelles, such as membranes, vesicles and microtubules. These organelles are processed with topological models and input parameters manually derived from the tomograms. After known organelles are extracted from the volume, all other watershed regions can be organized into homogeneous assemblies on the basis of their densities. To complete the process, all voxels in the volume are assigned either to the background or individual structures, which can then be extracted for visualization with any rendering technique. The user interface of the program is written in Java, and computational routines are written in C. For some operations, involving the visualization of the tomogram, we refer to existing software, either open or commercial. While the program runs, a history file is created, that allows all parameters and other data to be saved for the purposes of comparison or exchange. Initially, the program was developed for the segmentation of synapses, and organelles belonging to these structures have thus far been the principal targets modeled with JUST. Since each organelle is clustered independently from the rest of the volume, however, the program can accommodate new models of different organelles as well as tomograms of other types of preparations of tissue, such as cytoskeletal components in vitreous ice.
机译：我们正在提出一个基于客观标准的层析图像交互式分割程序，以产生可重复的结果。该策略首先使用3D中的分水岭算法对整个体积进行自动分割。分水岭地区通过有监督的分类连续聚类，从而可以分割已知的细胞器，例如膜，囊泡和微管。这些细胞器使用拓扑模型和从断层图手动得出的输入参数进行处理。从体积中提取已知细胞器后，所有其他分水岭地区都可以根据其密度组织成均匀的组件。为了完成该过程，将体积中的所有体素分配给背景或单个结构，然后可以使用任何渲染技术将其提取以进行可视化。程序的用户界面用Java编写，计算例程用C编写。对于涉及断层图可视化的某些操作，我们指的是开放或商用的现有软件。程序运行时，将创建一个历史文件，该历史文件允许保存所有参数和其他数据，以进行比较或交换。最初，该程序是针对突触的分割而开发的，迄今为止，属于这些结构的细胞器一直是用JUST建模的主要目标。但是，由于每个细胞器都独立于其余部分，因此该程序可以适应不同细胞器的新模型以及其他类型组织制剂的断层图，例如玻璃冰中的细胞骨架成分。

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