Imaging tissues and cells beyond the diffraction limit with structured illumination microscopy and Bayesian image reconstruction
Imaging tissues and cells beyond the diffraction limit with structured illumination microscopy and Bayesian image reconstruction
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DOI：
10.1093/gigascience/giy126
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发表时间：
2019-01-01
期刊：
影响因子：
9.2
通讯作者：
Hagen, Guy M.
中科院分区：
文献类型：
--
作者：
Pospisil, Jakub;Lukes, Tomas;Hagen, Guy M.
背景：结构照明显微镜（SIM）是光学荧光显微镜中的一类方法，可以实现光学切片和超分辨率效果。SIM是用常规荧光团标记的固定细胞或组织的高分辨率成像以及表达荧光蛋白构建的活细胞动态成像的一种有价值的方法。在SIM中，人们获得一组具有移动照明模式的图像。随后用图像分析算法处理这组图像，以产生具有减少失焦光（光学切片）和/或具有提高分辨率（超分辨率）的图像。研究结果：提出了五个完整的、免费的SIM数据集，包括原始数据和分析数据。我们报告了使用开源软件进行图像采集和分析的方法，以及用不同方法处理后产生的图像的示例。我们使用已建立的光学切片SIM和超分辨率SIM方法以及我们正在开发的较新的贝叶斯恢复方法处理数据。结论：目前正在积极开发各种SIM数据采集和处理方法，但SIM实验的完整原始数据通常不会发表。可公开获得的高质量原始数据以及处理结果示例将有助于研究人员开发SIM中的新方法。生物学家也会对我们获得的动物组织和细胞的高分辨率图像感兴趣。所有的数据都是用SIMToolbox处理的，这是一个开源的、免费的SIM软件解决方案。
Background: Structured illumination microscopy (SIM) is a family of methods in optical fluorescence microscopy that can achieve both optical sectioning and super-resolution effects. SIM is a valuable method for high-resolution imaging of fixed cells or tissues labeled with conventional fluorophores, as well as for imaging the dynamics of live cells expressing fluorescent protein constructs. In SIM, one acquires a set of images with shifting illumination patterns. This set of images is subsequently treated with image analysis algorithms to produce an image with reduced out-of-focus light (optical sectioning) and/or with improved resolution (super-resolution). Findings: Five complete, freely available SIM datasets are presented including raw and analyzed data. We report methods for image acquisition and analysis using open-source software along with examples of the resulting images when processed with different methods. We processed the data using established optical sectioning SIM and super-resolution SIM methods and with newer Bayesian restoration approaches that we are developing. Conclusions: Various methods for SIM data acquisition and processing are actively being developed, but complete raw data from SIM experiments are not typically published. Publically available, high-quality raw data with examples of processed results will aid researchers when developing new methods in SIM. Biologists will also find interest in the high-resolution images of animal tissues and cells we acquired. All of the data were processed with SIMToolbox, an open-source and freely available software solution for SIM.