Multi-site assessment of reproducibility in high-content live cell imaging data
type: Dataset
description: 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 Fi…
creative work status: completed
  type: DefinedTerm
  in defined term set: http://publications.europa.eu/resource/authority/dataset-status
  term code: COMPLETED
creator: Jianjiang Hu
creator: Xavier Serra-Picamal
  type: Person
  family name: Serra-Picamal
  given name: Xavier
creator: Gert-Jan Bakker
  type: Person
  family name: Bakker
  given name: Gert-Jan
creator: Marleen Van Troys
  type: Person
  family name: Van Troys
  given name: Marleen
creator: Sabina Winograd-katz
  type: Person
  family name: Winograd-katz
  given name: Sabina
creator: Nil Ege
  type: Person
  affiliation: The Francis Crick Institute
  family name: Ege
  given name: Nil
creator: Xiaowei Gong
  type: Person
  family name: Gong
  given name: Xiaowei
creator: Yuliia Didan
  type: Person
  family name: Didan
  given name: Yuliia
creator: Inna Grosheva
  type: Person
  family name: Grosheva
  given name: Inna
creator: Omer Polansky
  type: Person
  family name: Polansky
  given name: Omer
creator: Karima Bakkali
  type: Person
  family name: Bakkali
  given name: Karima
creator: Evelien Van Hamme
  type: Person
  family name: Van Hamme
  given name: Evelien
creator: Merijn van Erp
  type: Person
  family name: Erp
  given name: Merijn van
creator: Manon Vullings
  type: Person
  family name: Vullings
  given name: Manon
creator: Felix Weiss
  type: Person
  family name: Weiss
  given name: Felix
creator: Jarama Clucas
  type: Person
  affiliation: The Francis Crick Institute
  family name: Clucas
  given name: Jarama
creator: Anna Dowbaj
  type: Person
  affiliation: The Francis Crick Institute
  family name: Dowbaj
  given name: Anna
creator: Erik Sahai
  type: Person
  affiliation: The Francis Crick Institute
  family name: Sahai
  given name: Erik
creator: Christophe Ampe
  type: Person
  family name: Ampe
  given name: Christophe
creator: Benjamin Geiger
  type: Person
  family name: Geiger
  given name: Benjamin
creator: Peter Friedl
  type: Person
  family name: Friedl
  given name: Peter
creator: Matteo Bottai
  type: Person
  family name: Bottai
  given name: Matteo
creator: Staffan Strömblad
  type: Person
  family name: Strömblad
  given name: Staffan
date modified: 2023-05-30
date published: 2022-12-01
funding: Capture, dissemination and analysis of multiscale cell migration data for biological and clinical applications (MULTIMOT)
  type: Grant
  funder: European Commission
keywords: Medical and Health Sciences
  type: DefinedTerm
  term code: 3
keywords: Bioinformatics (Computational Biology)
  type: DefinedTerm
  term code: 10203
keywords: Biological Sciences
  type: DefinedTerm
  term code: 106
keywords: Systems biology
keywords: Bioinformatic methods development
license: https://creativecommons.org/licenses/by/4.0/
publisher: Karolinska Institutet
version: 0

PropertyValue
property ID: DOI
value: 10.17044/SCILIFELAB.21407402

Jianjiang Hu
type: Person
affiliation: Science for Life Laboratory
family name: Hu
given name: Jianjiang

Science for Life Laboratory
type: Organization

The Francis Crick Institute
type: Organization

European Commission
type: Organization

Karolinska Institutet
type: Organization