Key-Value pair template for annotation of datasets in OMERO for light- and electron microscopy data within the research group of Prof. Müller-Reichert

This are a two Key-Value pair templates used for the annotation of datasets in OMERO. They are tailored for light- and electron microcopy data for all research projects of the research group of Prof. T. Mueller-Reichert.  All members of the Core Facility Cellular Imaging agreed for using these templates to annotate data in OMERO. Furthermore, there are a corresponding public example datasets used in the publication "Setting up an institutional OMERO environment for bioimage data: perspectives from both facility staff and users" and are available here:

https://omero.med.tu-dresden.de/webclient/?show=dataset-1552 --> for lattice-light sheet microscopy

https://omero.med.tu-dresden.de/webclient/?show=dataset-1555--> for electron microscopy data

That templates are based on the REMBI recommendations (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8606015) and were developed during the PoL-Bio-Image Analysis Symposium in Dresden Aug 28th- Sept 1st in 2023 and further adapeted during the usage of OMERO. 

With every 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:

• fill the template with metadata
• select and copy the data range containing the Keys and Values
• open a new excel sheet and paste transpose in cell A1
• Important: cell A1 contains always the name 'dataset' and cell A2 contains the exact name of the dataset, which should be annotated in OMERO
• save the new excel sheet in csv-file (comma separated values) format

Examples can be seen in sheet 3 'csv_TOMO' and sheet 5 csv_TEM'.

Important note: The code has to be 8-Bit UCS transformation format (UTF-8) otherwise several characters (for example µ, %,°) might be not able to decode by the annotation script. We encountered this issue with old Microsoft-Office versions (MS Office 2016). 

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

See cross reference:

10.5281/zenodo.12546808 
Key-Value pair template for annotation of datasets in OMERO (PERIKLES study)

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