Key-Value pair template for annotation of datasets in OMERO (PERIKLES study)

This is a Key-Value pair template used for the annotation of datasets in OMERO. It is tailored for a research study (PERIKLES project) on the biocompatibility of newly designed biomaterials out of pericardial tissue for cardiovascular substitutes (https://doi.org/10.1063/5.0182672) conducted in the research department of Cardiac Surgery at the Faculty of Medicine Carl Gustav Carus at the Technische Universität Dresden . A corresponding public example dataset is used in the publication "Setting up an institutional OMERO environment for bioimage data: perspectives from both facility staff and users" and is available here

(https://omero.med.tu-dresden.de/webclient/?show=dataset-1557).

The template is based on the REMBI recommendations (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8606015) and it was developed during the PoL-Bio-Image Analysis Symposium in Dresden Aug 28th- Sept 1th 2023. 

With this template it is possible to create a csv-file, that can be used to annotate a dataset in OMERO using the annotation script (https://github.com/ome/omero-scripts/blob/develop/omero/annotation_scripts/).

How to use:

• select and copy the data range containing Keys and Values
• open a new excel sheet and paste transpose in column B1
• type in A1 'dataset'
• insert in A2 the exact name of the dataset, which should be annotated in OMERO
• save the new excel sheet in csv- (comma seperated values) file format

Example can be seen in sheet 1 'csv import'. Important note; the code has to be 8-Bit UCS transformation format (UTF-8) otherwise several characters (for example µ, %,°) might not be able to decode by the annotation script. We encountered this issue with old Microsoft Office versions (e.g. MS Office 2016). 

Note: By filling the values in the excel sheet, avoid the usage of decimal delimiter.

See cross reference:

10.5281/zenodo.12547566 Key-Value pair template for annotation of datasets in OMERO (light- and electron microscopy data within the research group of Prof. Mueller-Reichert)

10.5281/zenodo.12578084 Key-Value pair template for annotation in OMERO for light microscopy data acquired with AxioScan7 - Core Facility Cellular Imaging (CFCI)