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napari-nuclephaser documentation
================================

Welcome to the napari-nuclephaser documentation!

To learn how to install NuclePhaser, read installation instructions:

.. toctree::
   :maxdepth: 2
   :caption: Installation instructions

   Installation/Installation.rst

To learn how NuclePhaser can be used for biological tasks, navigate to these sections:

.. toctree::
   :maxdepth: 1
   :caption: Biological tasks guidelines

   Biological tasks guidelines/Population growth curves.rst
   Biological tasks guidelines/Individual cells tracking.rst

To learn more about the algorithms behind the project, navigate to general information sections:

.. toctree::
   :maxdepth: 1
   :caption: General information

   General information/Object detection overview.rst
   General information/Sliced inference overview.rst
   General information/Confidence threshold calibration.rst
   General information/Test-time augmentations (TTA).rst

To learn more about widgets and their functions, navigate to the widget page you need:

.. toctree::
   :maxdepth: 1
   :caption: Widgets

   Widgets/Predict on single image.rst
   Widgets/Predict on 1-stack.rst
   Widgets/Predict on 2-stack.rst
   Widgets/Calibrate with known number.rst
   Widgets/Calibrate with DAPI.rst
   Widgets/Calibrate with points.rst
   Widgets/Convert points to labels.rst
   Widgets/Count points on single image.rst