NL-Bioimaging: FAIR-DM

This project collects and maintains minimum information metadata templates designed and used in the National NL-Bioimaging initiative. The templates are based on the REMBI standards and contribute to FAIR bioimaging data in the Netherlands, together with data management in the OMERO database.

User metadata is an essential part of experimental data. Scientists need to understand underlying conditions and experimental procedures in order to model or investigate relevant biological questions. Currently, only a small fraction of the High Content SCreening (HCS) investigations are deposited for reuse by the community, and an even smaller fraction of that data is standards-compliant. For reusing data, scientists need to be able to understand how data was generated, under which experimental ...

A minimal metadata template for high content screening experiments in microscopy. The template is compliant with REMBI (Recommended Metadata for Biological Images) and the ISA framework (Investigations, Studies and Assays).

Here you will find guidelines for filling in MIHCSME metadata templates, as well as examples of published HCS studies that use MIHCSME.

Generic metadata template describing High Content Screening data that conform to the REMBI and ISA specification. LEI-MIHCSME empty template that can serve as basis for filling in metadata. This template was created and modified from templates produced by Leiden University.

Compound screen on 13 HepG2 -GFP reporter lines, to measure GFP protein induction, and cell death induction. Template and associated files describe High Content Screening experimental data that conform to the MIHCSME specification.

MIHCSME template example for IDR0022 dataset. Primary and validation RNAi screen using smartpool and single siRNAs to identify cell migratory regulators in Hs578T and MDA-MB-231 triple-negative breast cancer cells.

RNAi Screen of 100 candidate genes predicted to be involved in mitotic chromosome condensation. MIHCSME template example for IDR0002 dataset.

Compound screen on HepG2 CHOP-GFP reporter, to measure CHOP-GFP protein induction upon treatment with compounds. Template and associated files describe High Content Screening experimental data that conform to the MIHCSME specification.

An example template for screen published in IDR (idr0022, screenA).

An example template for screen published in IDR (idr0022, screenB).

An example template describing compound screen on HepG2 CHOP-GFP reporter .

An example template for screen published in IDR (idr0002, screenA).

This excel template is for use of describing HCS microscopy data. It was created based on ISA methodology and modified to conform REMBI recomandations.

An example of MIHCSME describing live cell imaging HepG2 -GFP reporter line.

An example of MIHCSME describing live cell imaging HepG2 -GFP reporter line, describing assay with cell death staining.

An overview of MIHCSME template components.

This file is associated with performed study and describes protocols used.

Associated library SOP file with metadata template.

This document is associated with metadata file and describes compounds used in this study.