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SciJava Ops Documentation 1.1.0
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‎docs/ops/doc/ParameterConversion.rst‎

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A :ref:`value <driving-values>` of SciJava Ops is flexibility, and flexibility is (in part) achieved through **parameter conversion**. At its core, parameter conversion allows *translation* of data stored in one data structure (e.g. an ImgLib2 ``RandomAccessibleInterval``) into a different data structure (e.g. an OpenCV ``Mat``) **on the fly**. This allows SciJava Ops to execute Ops backed by OpenCV code **on ImgLib2 data structures**.
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.. figure:: https://media.scijava.org/scijava-ops/1.0.1/parameter-conversion-opencv.svg
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.. figure:: https://media.scijava.org/scijava-ops/1.1.0/parameter-conversion-opencv.svg
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At matching time, parameter conversion is invoked when an Op matches a user request in name and in Op type, but differing in individual parameter types. In these situations, it looks for ``engine.convert`` Ops that could potentially convert the user's provided inputs into the required Op inputs, and the same, in the other direction, for the output.
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‎docs/ops/doc/examples/mesh_viz.rst‎

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In this example, we will use SciJava Ops to construct a 3D mesh from a binary dataset, passing the result into `3D Viewer`_ for visualization. We use the `bat cochlea volume`_ dataset (more information `here <https://imagej.net/images/bat-cochlea-volume.txt>`_) from the ImageJ sample images, which users can either download using the link or open from the ``File → Open Samples → Bat Cochlea Volume`` menu selection within Fiji.
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.. figure:: https://media.scijava.org/scijava-ops/1.0.1/mesh-visualization.png
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.. figure:: https://media.scijava.org/scijava-ops/1.1.0/mesh-visualization.png
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**Left**: The original binary bat cochlea volume, displayed as an Image. **Right**: The convex hull generated by SciJava Ops, overlaid on the original binary bat cochlea volume.
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‎docs/ops/doc/examples/volume_labeling.rst‎

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To use the script in the example first download the sample dataset `here`_. Next, open Fiji, the sample image and this scipt. Click **Run** to create the script parameter GUI,
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where you can customize some values to your own data, such as the channel names, channel position and image calibration values.
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.. figure:: https://media.scijava.org/scijava-ops/1.0.1/labeling_mesh_example_dialog.png
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.. figure:: https://media.scijava.org/scijava-ops/1.1.0/labeling_mesh_example_dialog.png
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:align: center
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Once the script has been configured click **OK** to start the analysis. The script will display two tables (one for each channel with the given channel name) and the labeling
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output for the puncta within nuclear regions only.
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.. figure:: https://media.scijava.org/scijava-ops/1.0.1/labeling_mesh_example_1.gif
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.. figure:: https://media.scijava.org/scijava-ops/1.1.0/labeling_mesh_example_1.gif
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Results of 3D nuclear puncta segmentation on the sample data.
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After the script completes two results tables will be displayed, one for each channel respectively. Each table contains measurements for the **size** of the label, the **volume** and the **sphericity**. Both the volume and sphericity Ops
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work on mesh objects, while the size Op works on the sample itself.
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.. figure:: https://media.scijava.org/scijava-ops/1.0.1/labeling_mesh_example_result_tables.png
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.. figure:: https://media.scijava.org/scijava-ops/1.1.0/labeling_mesh_example_result_tables.png
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The output result tables for the "Vif" and "Nuclei" channels.
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In addition to the result tables, the label imdage (also known as an *index image*) of the channel "A" data extracted from channel "B" regions is shown. Note that these labels are 3D (XYZ) and are used to create meshes for the geometry measurements.
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.. figure:: https://media.scijava.org/scijava-ops/1.0.1/labeling_mesh_example_2.gif
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.. figure:: https://media.scijava.org/scijava-ops/1.1.0/labeling_mesh_example_2.gif
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:width: 65%
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