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

dataset
posted on 01.12.2022, 08:07 authored by Jianjiang HuJianjiang Hu, Xavier Serra-Picamal, Gert-Jan BakkerGert-Jan Bakker, Marleen Van TroysMarleen Van Troys, Sabina Winograd-katz, Nil EgeNil Ege, Xiaowei Gong, Yuliia Didan, Inna Grosheva, Omer Polansky, Karima Bakkali, Evelien Van Hamme, Merijn van Erp, Manon Vullings, Felix Weiss, Jarama ClucasJarama Clucas, Anna Dowbaj, Erik SahaiErik Sahai, Christophe Ampe, Benjamin Geiger, Peter Friedl, Matteo Bottai, Staffan Strömblad

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.

Funding

Capture, dissemination and analysis of multiscale cell migration data for biological and clinical applications (MULTIMOT)

European Commission

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History

Publisher

Karolinska institutet; Radboud University Medical Center

Contact email

jianjiang.hu@ki.se