Merge pull request #48 from jburel/imaging_link

update to use new tool linking
elixir-europe · Jul 25, 2023 · 85b20aa · 85b20aa
2 parents eb9f8e7 + 6a62d0f
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diff --git a/pages/tool_assembly/omero_assembly.md b/pages/tool_assembly/omero_assembly.md
@@ -31,6 +31,9 @@ OMERO handles all your images in a secure central repository. Users can view, [o
 
 OMERO stores image metadata in a relational database and offers a more flexible structure based on HDF5 to store for example, analytical results. This allows analytical results generated by 3rd party softwares e.g. {% tool "cellprofiler" %}, {% tool "ilastik" %}, etc., to be stored alongside the images.
 
+Recommendations and software tools are being developed to capture acquisition metadata importable into OMERO e.g.
+{% tool "4dn-bina-ome-quarep" %}.
+
 
 {% include image.html file="ome_informatics.png" caption="Schematic overview of the OMERO tool assembly." alt="Schematic overview of the OMERO tool assembly." %}
 

diff --git a/pages/your_domain/bioimaging_data.md b/pages/your_domain/bioimaging_data.md
@@ -77,7 +77,7 @@ Unlike other domains, the bioimaging community has not yet agreed on a single st
 **Metadata**: If metadata are stored separately from the image data, the format of the metadata should follow the subject-specific standards regarding the schema, vocabulary or ontologies and storage format used such as:
 
   - [OME model](https://docs.openmicroscopy.org/ome-model/latest/) XML-based representation of microscopy data.
-  - [Quality assessment and Reproducibility in Light Microscopy (QUAREP-LiMi)](https://quarep.org/).
+  - {% tool "4dn-bina-ome-quarep" %}.
   - [REMBI](https://www.nature.com/articles/s41592-021-01166-8).