Accurate, precise modeling of cell proliferation kinetics from time-lapse imaging and automated image analysis of agar yeast culture arrays.
Accurate, precise modeling of cell proliferation kinetics from time-lapse imaging and automated image analysis of agar yeast culture arrays.
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通过延时成像和琼脂酵母培养阵列的自动化图像分析对细胞增殖动力学的准确，精确的建模。
DOI：
10.1186/1752-0509-1-3
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发表时间：
2007-01-08
影响因子：
--
通讯作者：
Hartman, John L 4th
中科院分区：
文献类型：
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作者：
Shah, Najaf A;Laws, Richard J;Wardman, Bradley;Zhao, Lue Ping;Hartman, John L 4th
全基因组突变菌株集合增加了对高通量细胞表型分析 (HTCP) 的需求。例如，研究人员使用 HTCP 通过评估 5000 个酿酒酵母基因缺失菌株的细胞增殖差异来研究基因缺失突变与其他化学或遗传扰动之间的相互作用。迄今为止，此类研究主要是定性的，使用琼脂细胞阵列对生长差异进行主观评分。基因相互作用的定量系统水平分析将通过更精确的 HTCP 方法来实现，例如通过光密度对液体培养物中的细胞增殖进行动力学分析。然而，与琼脂相比，处理液体培养物的要求使其相对麻烦且通量低。为了提高 HTCP 性能并提高定量相互作用的能力，开发了 YeastXtract 软件来自动分析细胞阵列图像。 YeastXtract 软件专为斑点琼脂培养物的动力学生长曲线分析而开发。琼脂培养阵列图像分析的准确性和精密度与液体培养物的 OD 测量相当。使用 YeastXtract，图像强度与斑点培养物的生物量在两个数量级上呈线性相关。因此，可以测量大约七代的细胞增殖，包括四到五代相对恒定的指数生长期。点面积归一化减少了总生长效率测量的变化。与经验方法相比，基于逻辑函数的增长模型提高了最大比速率测量的精度和准确度。逻辑函数模型对于数据稀疏性也更加稳健，这意味着需要更少的数据来获得准确、精确、定量的生长表型。点样到琼脂培养基上的微生物培养物广泛用于基因型-表型分析，但是以前还没有能够测量动态生长速率的定量 HTCP 方法。 YeastXtract 提供琼脂细胞培养阵列的客观、自动化、定量图像分析。将所得数据拟合到基于逻辑方程的增长模型中，可产生稳健、准确的增长率信息。这些方法允许将固体琼脂培养基上生长的细胞阵列的成像和自动图像分析纳入 HTCP 驱动的实验方法，例如基因相互作用网络的全局定量分析。
Genome-wide mutant strain collections have increased demand for high throughput cellular phenotyping (HTCP). For example, investigators use HTCP to investigate interactions between gene deletion mutations and additional chemical or genetic perturbations by assessing differences in cell proliferation among the collection of 5000 S. cerevisiae gene deletion strains. Such studies have thus far been predominantly qualitative, using agar cell arrays to subjectively score growth differences. Quantitative systems level analysis of gene interactions would be enabled by more precise HTCP methods, such as kinetic analysis of cell proliferation in liquid culture by optical density. However, requirements for processing liquid cultures make them relatively cumbersome and low throughput compared to agar. To improve HTCP performance and advance capabilities for quantifying interactions, YeastXtract software was developed for automated analysis of cell array images. YeastXtract software was developed for kinetic growth curve analysis of spotted agar cultures. The accuracy and precision for image analysis of agar culture arrays was comparable to OD measurements of liquid cultures. Using YeastXtract, image intensity vs. biomass of spot cultures was linearly correlated over two orders of magnitude. Thus cell proliferation could be measured over about seven generations, including four to five generations of relatively constant exponential phase growth. Spot area normalization reduced the variation in measurements of total growth efficiency. A growth model, based on the logistic function, increased precision and accuracy of maximum specific rate measurements, compared to empirical methods. The logistic function model was also more robust against data sparseness, meaning that less data was required to obtain accurate, precise, quantitative growth phenotypes. Microbial cultures spotted onto agar media are widely used for genotype-phenotype analysis, however quantitative HTCP methods capable of measuring kinetic growth rates have not been available previously. YeastXtract provides objective, automated, quantitative, image analysis of agar cell culture arrays. Fitting the resulting data to a logistic equation-based growth model yields robust, accurate growth rate information. These methods allow the incorporation of imaging and automated image analysis of cell arrays, grown on solid agar media, into HTCP-driven experimental approaches, such as global, quantitative analysis of gene interaction networks.