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update to use new tool linking #48

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merged 3 commits into from
Jul 25, 2023
Merged

update to use new tool linking #48

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6cec01c
add link to 4dn tools
jburel Jul 24, 2023
1955532
link to resources
jburel Jul 24, 2023
6a62d0f
add missing dot
jburel Jul 24, 2023
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3 changes: 3 additions & 0 deletions pages/tool_assembly/omero_assembly.md
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Expand Up @@ -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." %}

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2 changes: 1 addition & 1 deletion pages/your_domain/bioimaging_data.md
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Expand Up @@ -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).


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