Algorithms
==========

.. currentmodule:: brainlit.algorithms.generate_fragments

Fragment Generation
-------------------

.. autoapiclass:: state_generation
	:members:
.. autoapifunction:: get_seed
.. autoapifunction:: get_img_T1
.. autoapifunction:: thres_from_gmm
.. autoapifunction:: fast_marching_seg
.. autoapifunction:: level_set_seg
.. autoapifunction:: connected_threshold
.. autoapifunction:: confidence_connected_threshold
.. autoapifunction:: neighborhood_connected_threshold
.. autoapifunction:: otsu
.. autoapifunction:: gmm_seg

.. currentmodule:: brainlit.algorithms.connect_fragments

Connect Fragments
-----------------
.. autoapiclass:: ViterBrain
	:members:


.. currentmodule:: brainlit.algorithms.trace_analysis

Trace Analysis
--------------

.. autoapifunction:: speed
.. autoapifunction:: curvature
.. autoapifunction:: torsion
.. autoapiclass:: CubicHermiteChain
	:members:
.. autoapiclass:: GeometricGraph
	:members:
.. autoapifunction:: compute_parameterization

.. currentmodule:: brainlit.algorithms.detect_somas

Soma Detection
--------------

.. autoapifunction:: find_somas