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

This Key-Value pair template is used for the data documentation during imaging experiments and the later data annotation in OMERO. It is tailored for the usage and image acquisition at the slide scanning system Zeiss AxioScan 7 in the Core Facility Cellular Imaging (CFCI). It contains important metadata of the imaging experiment, which are not saved in the corresponding imaging files. All users of the Core Facility Cellular Imaging are trained to use that file to document their imaging parameters directly during the data acquisition with the possibility for a later upload to OMERO. Furthermore, there is a corresponding public example image 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=image-33248

This template was developed by the CFCI staff during the setup and usage of the AxioScan 7 and is based on the REMBI recommendations (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8606015).

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

How to use:

• fill the template sheet  with your 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 image/dataset, which should be annotated in OMERO
• save the new excel sheet in csv-file (comma separated values) format

An example can be seen in sheet 3 'csv_AxioScan'.

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

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