Workflow guides
===============

RosettaX is easiest to understand when each workflow is treated as a separate
modeling question.

* :doc:`fluorescence` explains the log-log fluorescence regression and saved payload.
* :doc:`scattering` explains the optical assumptions, material handling, and linear instrument-response fit.
* :doc:`systems` catalogs flow-cytometer detector systems and 3D geometry figures.
* :doc:`apply` explains how saved calibrations are validated and applied to new FCS files.

.. toctree::
    :maxdepth: 1

    fluorescence
    scattering
    systems
    apply
