Multi-site assessment of reproducibility in high-content live cell imaging data

This dataset contains the raw images as well as the analysis pipelines and scripts used in the paper "Multi-site assessment of reproducibility in high-content live cell imaging data". The Original data-2D.rar file contains the raw timelapse images of HT1080 cell line stably expressing H2B-EGFP and Lifeact-mCherry seeded on collagen I coated glass surface. Migration behavior of the cells was recorded in 5 min intervals for 6 h with fluorescent light microscopes equipped with environmental chamber. The experiment was performed by 3 labs, 3 person in each lab, 3 independent experiments by each person, 3 technical replicates in each experiment, and two conditions (control and ROCK inhibition) for each technical repliates. The Data processing and analysis-2D.rar file contains the Matlab, CellProfiler, ImageJ, and R pipelines and scripts used in this study to process, quantify, and analyze the images. Detailed procedure could be found in the "Image processing and analysis procedures.txt" file within this .rar file. The 3D Image data from Lab 1.zip and 3D Image data from Lab 2.zip contain the raw images and the quantified results of the 3D migration assay from Lab 1 and Lab 2, respectively. The experiment was performed with HT1080 cell line stably expressing H2B-EGFP and Lifeact-mCherry embedded in 2.5mg/ml or 6mg/ml collagen I gels. The invasion of the cells from 3D spheroid was recorded with confocal microscopy 24 h after seeding. The experiment was performed by 2 labs, 3 independent experiments in each lab, 3 technical replicates in each experiment, and two conditions (2.5 mg/ml and 6 mg/ml of collagen I) for each technical repliates. The Meta data of the 3D experiment.zip contains the meta data of the 3D image data from Lab 1 (Radboudumc) and Lab 2 (Crick) as well as the software to read the meta data. After unzipping, ISAcreator program should be used to read the ISAfiles of Lab 1 or Lab 2. The Fiji Plugins and parameters for 3D image data analysis.rar contains the Fiji plugins and also the parameters used during the 3D image data analysis. The 3D Data Analysis Scripts.rar contains the R scripts used in this study to analyze the 3D data set, as well as the quantified results needed by the R scripts. The Supplementary Materials 2-8.rar contains 2D experimental protocol (supplementary materials 2-4), 2D experimental survey (supplementary materials 3), and 3D experimental and image analysis protocols (supplementary materials 5-8) that are used in this study. We encourage reuse using the same CC BY 4.0 License.本数据集包含发表于论文《高内涵活细胞成像数据可重复性的多中心评估》（Multi-site assessment of reproducibility in high-content live cell imaging data）中的原始图像、分析流程与脚本。 Original data-2D.rar压缩包内含稳定表达H2B-EGFP与Lifeact-mCherry的HT1080细胞系，接种于I型胶原蛋白包被玻璃表面后的延时拍摄原始图像。实验采用配备环境控制舱的荧光显微镜，以5分钟为间隔记录总时长6小时的细胞迁移行为。本次实验由3个实验室完成，每个实验室配备3名实验人员，每名人员开展3次独立实验，每次实验设置3个技术重复，每个技术重复包含对照组与ROCK抑制剂处理组两种实验条件。 Data processing and analysis-2D.rar压缩包包含本研究用于图像处理、定量与分析的Matlab、CellProfiler、ImageJ及R流程与脚本，详细操作步骤可参见该压缩包内的"Image processing and analysis procedures.txt"文件。 3D Image data from Lab 1.zip与3D Image data from Lab 2.zip分别包含来自实验室1与实验室2的3D迁移实验原始图像及定量结果。本次实验使用稳定表达H2B-EGFP与Lifeact-mCherry的HT1080细胞系，将其包埋于2.5mg/ml或6mg/ml的I型胶原蛋白凝胶中；接种后24小时，采用共聚焦显微镜记录细胞从3D细胞球体的侵袭行为。该实验由2个实验室完成，每个实验室开展3次独立实验，每次实验设置3个技术重复，每个技术重复包含2.5mg/ml与6mg/ml I型胶原蛋白两种凝胶浓度条件。 Meta data of the 3D experiment.zip压缩包包含来自Radboudumc（实验室1）与Crick（实验室2）的3D图像数据元数据，以及读取元数据所需的配套软件。解压后，可使用ISAcreator程序读取实验室1或实验室2的ISA文件。 Fiji Plugins and parameters for 3D image data analysis.rar压缩包包含本研究用于3D图像数据分析的Fiji插件及分析过程中使用的参数配置。 3D Data Analysis Scripts.rar压缩包包含本研究用于分析3D数据集的R脚本，以及R脚本运行所需的定量结果文件。 Supplementary Materials 2-8.rar压缩包包含本研究使用的2D实验方案（补充材料2-4）、2D实验调研（补充材料3），以及3D实验与图像分析方案（补充材料5-8）。 本数据集遵循CC BY 4.0协议，欢迎同行复用。