******** Tutorial ******** .. _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