Colonyzer: automated quantification of micro-organism growth characteristics on solid agar.
Colonyzer: automated quantification of micro-organism growth characteristics on solid agar.
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DOI：
10.1186/1471-2105-11-287
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发表时间：
2010-05-28
影响因子：
3
通讯作者：
Lydall DA
中科院分区：
文献类型：
--
作者：
Lawless C;Wilkinson DJ;Young A;Addinall SG;Lydall DA
比较固体琼脂上不同微生物培养物阵列的生长速率的高通量筛选是量化遗传相互作用的有用且快速的方法。生长速率是一种信息丰富的表型，可以通过接种后一次或多次测量细胞密度来估计。可以通过将培养物接种到琼脂上并通过板扫描或摄影经常捕获细胞密度（尤其是在整个指数生长期）并用简单的动态模型（例如逻辑生长模型）总结生长来进行精确估计。为了对这种模型进行参数化，需要一种强大的图像分析工具，能够从板照片中捕获各种细胞密度。 Colonyzer 是图像分析算法的集合，用于自动量化固体琼脂上生长的微生物培养物的大小、粒度、颜色和位置。由于使用混合高斯模型进行图像分割，基于像素强度进行全板阈值处理，Colonyzer 对稀释液体培养物接种（点样）后拍摄的极低细胞密度具有独特的敏感性。 Colonyzer 对轻微的实验缺陷具有鲁棒性，并可校正照明梯度，否则会在无需成像虚拟板的情况下对细胞密度估计引入空间偏差。 Colonyzer 足够通用，足以量化以任何矩形阵列格式生长的培养物，无论是在用密集接种物固定后生长，还是以斑点培养物的不规则形态特征生长。 Colonyzer 是使用开源包开发的：Python、RPy 和 Python Imaging Library，其源代码和文档可在 GNU 通用公共许可证下的 SourceForge 上获取。 Colonyzer 可适应特定要求：例如自动检测条纹板上不规则位置的培养物以供机器人拾取，或通过禁用照明校正或颜色测量等组件来减少分析时间。 Colonyzer 可以通过全基因组扫描期间捕获的大批量微生物培养物图像，在高度稀释的液体点接种后以及更集中的钉扎接种后可观察到的各种细胞密度中，自动量化培养物的生长情况。 Colonyzer 是开源的，允许用户对其进行评估、使其适应特定的研究要求并为其开发做出贡献。
High-throughput screens comparing growth rates of arrays of distinct micro-organism cultures on solid agar are useful, rapid methods of quantifying genetic interactions. Growth rate is an informative phenotype which can be estimated by measuring cell densities at one or more times after inoculation. Precise estimates can be made by inoculating cultures onto agar and capturing cell density frequently by plate-scanning or photography, especially throughout the exponential growth phase, and summarising growth with a simple dynamic model (e.g. the logistic growth model). In order to parametrize such a model, a robust image analysis tool capable of capturing a wide range of cell densities from plate photographs is required. Colonyzer is a collection of image analysis algorithms for automatic quantification of the size, granularity, colour and location of micro-organism cultures grown on solid agar. Colonyzer is uniquely sensitive to extremely low cell densities photographed after dilute liquid culture inoculation (spotting) due to image segmentation using a mixed Gaussian model for plate-wide thresholding based on pixel intensity. Colonyzer is robust to slight experimental imperfections and corrects for lighting gradients which would otherwise introduce spatial bias to cell density estimates without the need for imaging dummy plates. Colonyzer is general enough to quantify cultures growing in any rectangular array format, either growing after pinning with a dense inoculum or growing with the irregular morphology characteristic of spotted cultures. Colonyzer was developed using the open source packages: Python, RPy and the Python Imaging Library and its source code and documentation are available on SourceForge under GNU General Public License. Colonyzer is adaptable to suit specific requirements: e.g. automatic detection of cultures at irregular locations on streaked plates for robotic picking, or decreasing analysis time by disabling components such as lighting correction or colour measures. Colonyzer can automatically quantify culture growth from large batches of captured images of microbial cultures grown during genome-wide scans over the wide range of cell densities observable after highly dilute liquid spot inoculation, as well as after more concentrated pinning inoculation. Colonyzer is open-source, allowing users to assess it, adapt it to particular research requirements and to contribute to its development.
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影响因子：
2.1
作者：
Oliphant, Travis E.
通讯作者：
Oliphant, Travis E.
一种基于高斯混合模型的图像阈值处理新方法
影响因子：
4
作者：
Huang, Zhi-Kai;Chau, Kwok-Wing
通讯作者：
Chau, Kwok-Wing
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。
影响因子：
--
作者：
Shah, Najaf A;Laws, Richard J;Wardman, Bradley;Zhao, Lue Ping;Hartman, John L 4th
通讯作者：
Hartman, John L 4th
影响因子：
12.3
作者：
Collins SR;Schuldiner M;Krogan NJ;Weissman JS
通讯作者：
Weissman JS
影响因子：
2.7
作者：
Lamprecht, Michael R.;Sabatini, David M.;Carpenter, Anne E.
通讯作者：
Carpenter, Anne E.