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Tutorial
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.. _utils_tutorials:
Utils
=====
Tutorials showcasing how to use the utils folder.
.. toctree::
:maxdepth: 1
notebooks/utils/uploading_brains
notebooks/utils/downloading_brains
notebooks/utils/downloading_benchmarking
notebooks/utils/uploading_benchmarking
.. _pipeline_tutorials:
Pipelines
=========
.. _BrainLine_tutorials:
BrainLine: Whole-Brain Fluorescence Volume Analysis Pipeline
------------------------------------------------------------
Leverage `ilastik `_ to perform axon detection and soma detection on brain images, and combine with `CloudReg `_ image registration for visualization and analysis.
.. toctree::
:maxdepth: 1
notebooks/pipelines/BrainLine/axon_analysis
notebooks/pipelines/BrainLine/soma_analysis
Semi-automatic Annotation Pipeline
----------------------------------
Demonstrate pulling data and pushing traced annotations.
.. toctree::
:maxdepth: 1
notebooks/pipelines/seg_pipeline_demo
Segmentation
------------
Notebooks showing how to manually and automatically segment data.
.. toctree::
:maxdepth: 1
notebooks/pipelines/manual_segmentation
notebooks/pipelines/tubes_feature_extraction_demo
.. _algorithm_tutorials:
Algorithms
==========
Adaptive Thresholding
---------------------
Demonstrate region growing methods using GMM and simple ITK.
.. toctree::
:maxdepth: 1
notebooks/algorithms/adaptive_thresh_tutorial.ipynb
Connecting Fragments
---------------------
Demonstrate fragment path connections using Viterbi algorithm on a simple grid example.
.. toctree::
:maxdepth: 1
notebooks/algorithms/viterbi_tutorial.ipynb
notebooks/algorithms/viterbi2_tutorial.ipynb
Trace Analysis
--------------
Demonstrate estimation of curvature and torsion on simple curve, and fitting splines to a neuron.
.. toctree::
:maxdepth: 1
notebooks/algorithms/spline_fxns_tutorial.ipynb
notebooks/algorithms/view_swc_spline.ipynb
notebooks/algorithms/biccn_demo.ipynb
Soma Detection
--------------
Demonstrate simple soma detection algorithm on known somas in Janelia dataset, brain1.
.. toctree::
:maxdepth: 1
notebooks/algorithms/detect_somas.ipynb
.. _preprocessing_tutorials:
Preprocessing
=============
.. toctree::
:maxdepth: 1
notebooks/preprocessing/connectedcomponents
notebooks/preprocessing/gaborfilter
.. _viz_tutorials:
Vizualization
=============
These tutorials demonstrate tools to load and visualize data from s3 buckets or .swc files.
.. toctree::
:maxdepth: 1
notebooks/visualization/loading
notebooks/visualization/neighborhood_visualization_demo