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fix doc failure
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jburel committed May 20, 2022
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2 changes: 1 addition & 1 deletion docs/index.rst
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QuPath
======

QuPath is a free open-source cross-platform software application designed for bioimage analysis - and specifically to meet the needs of whole slide image analysis and digital pathology. We demonstrate how to integrate QuPath and OMERO using the User Interface. For more details, go to \ https://github.com/qupath/qupath/wiki/
QuPath is a free open-source cross-platform software application designed for bioimage analysis - and specifically to meet the needs of whole slide image analysis and digital pathology. We demonstrate how to integrate QuPath and OMERO using the User Interface. For more details, go to `QuPath Wiki page <https://github.com/qupath/qupath/wiki/>`_.

Contents:

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10 changes: 5 additions & 5 deletions docs/qupath.rst
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- IDR project referenced as `idr0018 <https://idr.openmicroscopy.org/search/?query=Name:idr0018>`_. Note that the data also have been imported into an OMERO.server where the possibility to write ROIs/annotations exists (not the IDR server itself). See the ``Step-by-step`` section for further details.

- Video showing the usage of the QuPath OMERO extension https://www.youtube.com/watch?v=IffQ18ZQ3mI
- QuPath documentation describing the QuPath OMERO extension https://qupath.readthedocs.io/en/latest/docs/advanced/omero.html
- `Video <https://www.youtube.com/watch?v=IffQ18ZQ3mI>`_ showing the usage of the QuPath OMERO extension
- QuPath documentation describing the `QuPath OMERO extension <https://qupath.readthedocs.io/en/latest/docs/advanced/omero.html>`_.

- Plugin ``ome-omero-roitool`` **v0.2.4** for import and export of ROIs to or from OMERO using OME-XML format. The ``ome-omero-roitool-xxx.zip`` under Releases also contains the scripts for export and import of ROIs from/to QuPath in OME-XML format. For precise installation steps, see below the ``Step-by-step`` section.

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Setup
-----

- Download QuPath **v0.3.0** from https://github.com/qupath/qupath/releases/tag/v0.3.0.
- Download the **v0.3.0** OMERO extension for QuPath from https://github.com/qupath/qupath-extension-omero/releases.
- Install the OMERO extension as described in https://github.com/qupath/qupath-extension-omero#qupath-omero-extension.
- Download QuPath `v0.3.0 <https://github.com/qupath/qupath/releases/tag/v0.3.0>`_.
- Download the `OMERO extension for QuPath <https://github.com/qupath/qupath-extension-omero/releases>`_ v0.3.0.
- Install the OMERO extension as described in `qupath-omero-extension <https://github.com/qupath/qupath-extension-omero>`_.

Step-by-step
------------
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