Graphical methods for quantifying macromolecules through bright field imaging.
Graphical methods for quantifying macromolecules through bright field imaging.
复制标题
DOI：
10.1093/bioinformatics/btn426
复制
发表时间：
2009-04-15
期刊：
影响因子：
--
通讯作者：
Parvin B
中科院分区：
文献类型：
--
作者：
Chang H;DeFilippis RA;Tlsty TD;Parvin B
用抗体和/或特殊染色剂染色的生物样品的明场成像提供了用于可视化各种大分子的快速方案。然而，由于样品固定的变化、颜色成分引入的模糊性以及成像仪器的有限动态范围，这种样品染色和成像方法很少用于直接定量分析。我们证明，通过颜色信号的分解，可以逐个细胞地对染色进行评分。我们已将我们的方法应用于从两个不同群体获得的组织学正常乳腺组织活检中生长的成纤维细胞。最初，通过将彩色图像转换为灰度并检测暗椭圆特征来分割核区域。随后，通过图割算法优化的颜色分解模型来量化染色强度。在极少数情况下，由于样品制备而导致核信号显着改变，可以验证和纠正核分割。最后，分段染色图案与基于区域的镶嵌后的每个核区域相关联。与经典的非负矩阵分解相比，所提出的方法：（i）改进了颜色分解，（ii）具有更好的抗噪性，（iii）对初始条件更不变，（iv）具有优越的计算性能。联系方式：hchang@lbl.gov
Bright field imaging of biological samples stained with antibodies and/or special stains provides a rapid protocol for visualizing various macromolecules. However, this method of sample staining and imaging is rarely employed for direct quantitative analysis due to variations in sample fixations, ambiguities introduced by color composition and the limited dynamic range of imaging instruments. We demonstrate that, through the decomposition of color signals, staining can be scored on a cell-by-cell basis. We have applied our method to fibroblasts grown from histologically normal breast tissue biopsies obtained from two distinct populations. Initially, nuclear regions are segmented through conversion of color images into gray scale, and detection of dark elliptic features. Subsequently, the strength of staining is quantified by a color decomposition model that is optimized by a graph cut algorithm. In rare cases where nuclear signal is significantly altered as a result of sample preparation, nuclear segmentation can be validated and corrected. Finally, segmented stained patterns are associated with each nuclear region following region-based tessellation. Compared to classical non-negative matrix factorization, proposed method: (i) improves color decomposition, (ii) has a better noise immunity, (iii) is more invariant to initial conditions and (iv) has a superior computing performance. contact: hchang@lbl.gov
登录
查看更多内容
影响因子：
2.5
作者：
GOLDBERG, AV;TARJAN, RE
通讯作者：
TARJAN, RE
影响因子：
4.6
作者：
Papadakis, AN;Stathopoulos, E;Balas, C
通讯作者：
Balas, C
影响因子：
64.8
作者：
Lee, DD;Seung, HS
通讯作者：
Seung, HS
影响因子：
4.6
作者：
Yang, Q;Parvin, B
通讯作者：
Parvin, B
DOI：
10.1109/34.87344
发表时间：
1991-06-01
影响因子：
23.6
作者：
VINCENT, L;SOILLE, P
通讯作者：
SOILLE, P