From 3852e2df97e0f0e9bb58f4a6020f992a257179dc Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 27 Nov 2024 15:20:25 +0000 Subject: [PATCH] Add https://zenodo.org/records/12547566 --- resources/nfdi4bioimage.yml | 70 +++++++++++++++++++++++++++++++++++++ 1 file changed, 70 insertions(+) diff --git a/resources/nfdi4bioimage.yml b/resources/nfdi4bioimage.yml index 6e5c496f..4dd736c9 100644 --- a/resources/nfdi4bioimage.yml +++ b/resources/nfdi4bioimage.yml @@ -8756,3 +8756,73 @@ resources: url: - https://zenodo.org/records/14197622 - https://doi.org/10.5281/zenodo.14197622 + +- authors: "Fabig, Gunar, Jannasch, Anett, Okafornta, Chukwuebuka, Boissonnet, Tom,\ + \ Schmidt, Christian, Bortolomeazzi, Michele, Fuchs, Vanessa Aphaia Fiona, Koeckert,\ + \ Maria, Poddar, Aayush, Vogel, Martin, Schwarzbach, Hanna-Margareta, Vogelsang,\ + \ Andy, Gerlach, Michael, Nobst, Anja, M\xFCller-Reichert, Thomas, Tulok, Silke" + description: '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) + +  ' + license: cc-by-4.0 + name: "Key-Value pair template for annotation of datasets in OMERO for light- and\ + \ electron microscopy data within the research group of Prof. M\xFCller-Reichert" + num_downloads: 12 + publication_date: '2024-06-26' + submission_date: '2024-11-27T15:20:23.287340' + url: + - https://zenodo.org/records/12547566 + - https://doi.org/10.5281/zenodo.12547566 + \ No newline at end of file