CIL:45870, Homo sapiens. In Cell Image Library

Gustafsdottir et al. (doi:10.1371/journal.pone.0080999) have developed a multiplex cytological profiling assay that "paints the cell" with as many fluorescent markers as possible without compromising our ability to extract rich, quantitative profiles in high throughput. The assay detects seven major cellular components. In a pilot screen of bioactive compounds, the assay detected a range of cellular phenotypes and it clustered compounds with similar annotated protein targets or chemical structure based on cytological profiles. The results demonstrate that the assay captures subtle patterns in the combination of morphological labels, thereby detecting the effects of chemical compounds even though their targets are not stained directly. This image-based assay provides an unbiased approach to characterize compound- and disease-associated cell states to support future probe discovery.

Using the cell-painting assay, the Broad Institute has assembled a reference dataset of profiles for U2OS osteosarcoma cells treated with ~30,000 compounds. The compound collection includes DOS-derived compounds (20,000), as well as chemically diverse MLI compounds with biologically diverse performance identified through analysis of PubChem (10,000), and known bioactive compounds to serve as landmarks (2,500). The DOS compounds consist of structurally diverse and stereochemically rich compounds with structures distinct from the current MLSMR. The compound collection also includes 267 distinct compounds nominated by MLPCN Centers from projects for which the Centers would like to identify new chemical series with similar activities.

The experiment consists of 413 microtiter plates. Each plate has 384 wells. Each well has 9 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale 16-bit TIFF image file.

Gustafsdottir 等人（doi:10.1371/journal.pone.0080999）开发了一种多重细胞学谱分析检测技术，即“给细胞上色”的检测方法，可在不损害高通量提取丰富定量谱图能力的前提下，使用尽可能多的荧光标记物标记细胞。该检测方法可靶向七种主要细胞组分。在一项生物活性化合物的先导筛选实验中，该检测方法可识别多种细胞表型，并能基于细胞学谱图将具有相似注释蛋白靶点或化学结构的化合物进行聚类。研究结果表明，该检测方法能够捕捉形态学标记组合中的细微模式，因此即便化合物的作用靶点未被直接染色，也可检测其产生的细胞效应。这种基于图像的检测方法提供了一种无偏倚的研究途径，可用于表征化合物及疾病相关的细胞状态，为未来的探针发现提供支撑。

依托该细胞上色（cell-painting assay）检测技术，博德研究所（Broad Institute）构建了一套参考数据集，涵盖经约30000种化合物处理的U2OS骨肉瘤细胞的谱图数据。该化合物库包含三类组分：DOS来源化合物（20000种）、通过PubChem分析筛选得到的化学结构多样且生物学活性分布广泛的MLI化合物（10000种），以及作为参照物的已知生物活性化合物（2500种）。其中DOS化合物结构多样且立体化学特征丰富，其分子结构与当前MLSMR库中的化合物存在显著差异。此外，该化合物库还包含MLPCN中心提名的267种独特化合物，这些化合物来自相关研究项目，相关项目希望借此识别具有相似活性的新型化学系列。

该实验共涉及413块微孔板，每块板包含384个培养孔，每个孔采集9个成像视场。每个视场通过5个成像通道（检测波长）完成成像，每个通道的图像均以独立的灰度16位TIFF图像文件存储。