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RTD: add page for 2024 Ops paper
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‎docs/conf.py‎

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html_static_path = []
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# Add the SciJava ops logo
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html_logo = "ops/images/scijava_logo.svg"
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html_logo = "ops/images/scijava-ops.svg"
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html_theme_options = {
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"logo_only": True,
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"display_version": False,

‎docs/ops/doc/Paper2024.rst‎

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SciJava Ops: An Improved Algorithms Framework for Fiji and Beyond
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=================================================================
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This page serves as a stable location for the SciJava Ops Paper and associated resources. If you find SciJava Ops useful, please cite our (forthcoming) paper:
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Python (scyjava)
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----------------
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This use case illustrates the ease with which SciJava Ops can be accessed in Python, showcasing ``OpEnvironment`` setup and simple image processing. The full workflow can be found in the `scyjava use case <examples/scyjava.html>`_.
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+--------------+--------------------------------------------------------------------------------------+
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| |scyj_thumb| |`3D 3T3 Mouse Nucleus <https://media.imagej.net/scijava-ops/1.0.0/3t3_nucleus.tif>`_ |
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+--------------+--------------------------------------------------------------------------------------+
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Fluorescence Lifetime Image Analysis
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------------------------------------
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This use case illustrates how SciJava Ops can be freely extended with additional algorithms libraries, making use of the SciJava framework for convenience and performance in FLIM analysis. The full workflow can be found in the `FLIM use case <examples/flim_analysis.html>`_.
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+--------------+----------------------------------------------------------------------------------+
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| |flim_thumb| | `BPAE cells <https://media.imagej.net/scijava-ops/1.0.0/flim_example_data.sdt>`_ |
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+--------------+----------------------------------------------------------------------------------+
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Spatially Adapted Colocalization Analysis
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-----------------------------------------
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This use case illustrates the novel scientific utility of the SciJava Ops Image library using powerful algorithms for pixel colocalization. The full workflow can be found in the `SACA use case <examples/deconvolution.html>`_.
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+--------------+----------------------------------------------------------------------------------------------------------------------+
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| |saca_thumb| | `HeLa cell expressing HIV gene products <https://media.imagej.net/scijava-ops/1.0.0/hela_hiv_gag_ms2_mcherry.tif>`_ |
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+--------------+----------------------------------------------------------------------------------------------------------------------+
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Deconvolution
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-------------
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This use case illustrates the novel scientific utility of the SciJava Ops Image library using powerful algorithms for image deconvolution. The full workflow can be found in the `deconvolution use case <examples/deconvolution.html>`_.
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+---------------+-------------------------------------------------------------------------------------------+
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| |decon_thumb| | `3D HeLa nucleus <https://media.imagej.net/scijava-ops/1.0.0/hela_nucleus.tif>`_ |
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+---------------+-------------------------------------------------------------------------------------------+
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.. |decon_thumb| image:: https://media.imagej.net/scijava-ops/1.0.0/hela_nucleus_thumbnail.png
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:width: 10em
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.. |flim_thumb| image:: https://media.imagej.net/scijava-ops/1.0.0/flim_example_input_56.png
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:width: 10em
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.. |saca_thumb| image:: https://media.imagej.net/scijava-ops/1.0.0/hela_hiv_gag_ms2_mcherry_thumbnail.png
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:width: 10em
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.. |scyj_thumb| image:: https://media.imagej.net/scijava-ops/1.0.0/3t3_nucleus_thumbnail.png
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:width: 10em
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‎docs/ops/doc/index.rst‎

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WritingYourOwnOpPackage
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Migrating Ops Written for ImageJ Ops<MigratingFromImageJOps>
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.. toctree::
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:maxdepth: 2
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:caption: 📚 Papers
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Paper2024
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Indices and tables
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==================
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‎docs/ops/images/scijava-ops.svg‎

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