API reference
=============

Core functions
--------------

.. automodule:: motila.motila
   :members: process_stack, batch_process_stacks, batch_collect
   :undoc-members:
   :show-inheritance:

Additional functions
--------------------

.. currentmodule:: motila.motila

.. autofunction:: hello_world
.. autofunction:: calc_projection_range
.. autofunction:: plot_2D_image
.. autofunction:: plot_2D_image_as_tif
.. autofunction:: plot_histogram
.. autofunction:: plot_histogram_of_projections
.. autofunction:: plot_projected_stack
.. autofunction:: plot_projected_stack_as_tif
.. autofunction:: get_stack_dimensions
.. autofunction:: extract_and_register_subvolume
.. autofunction:: extract_subvolume
.. autofunction:: spectral_unmix
.. autofunction:: histogram_equalization
.. autofunction:: histogram_equalization_on_projections
.. autofunction:: histogram_matching
.. autofunction:: histogram_matching_on_projections
.. autofunction:: median_filtering_on_projections
.. autofunction:: circular_median_filtering_on_projections
.. autofunction:: single_slice_median_filtering
.. autofunction:: single_slice_circular_median_filtering
.. autofunction:: gaussian_blurr_filtering_on_projections
.. autofunction:: single_slice_gaussian_blurr_filtering
.. autofunction:: z_max_project
.. autofunction:: compare_histograms
.. autofunction:: plot_intensities
.. autofunction:: reg_2D_images
.. autofunction:: binarize_2D_images
.. autofunction:: remove_small_blobs
.. autofunction:: plot_pixel_areas
.. autofunction:: motility


Utility functions
-----------------

.. automodule:: motila.utils
   :members:
   :undoc-members:
   :show-inheritance: