brainlit
  • Brainlit
    • Motivation
    • Installation
      • Environment
      • Install from pypi
      • Install from source
    • How to use Brainlit
      • Data setup
      • Create a session
    • Features
      • Registration
    • Core
      • Push and Pull Data
      • Visualize
      • Manually Segment
      • Automatically and Semi-automatically Segment
    • Tests
    • Contributing
    • Credits
  • Tutorial
    • Utils
      • Uploading Brain Images from data in the Octree format.
      • Downloading Brain data tutorial
      • Download benchmarking data from S3 with Neuroglancer
      • Download raw benchmarking data
      • Upload benchmarking data to S3 with Neuroglancer
    • Pipelines
      • Semi-automatic Annotation Pipeline
      • Segmentation
    • Algorithms
      • Adaptive Thresholding
      • Connecting Fragments
      • Trace Analysis
      • Soma Detection
    • Preprocessing
      • Connected Component Manipulation
      • Gabor Filters
    • Vizualization
      • Loading neurons from s3
      • Visualization of Neighborhoods Tutorial
  • Reference
    • Algorithms
      • Fragment Generation
      • Connect Fragments
      • Trace Analysis
      • Soma Detection
    • Feature Extraction
      • NeighborhoodFeatures
    • Preprocessing
      • Image Processing
      • Image Filters
      • Segmentation Processing
    • Registration
      • File IO
      • Image Data
      • Transformers
      • Visualization
    • Utility
      • Data Helper Methods
      • S3 Helper Methods
    • Visualization
      • Trace Visualization
  • Napari Plugin
    • ViterBrain Napari Plugin Installation
    • How to Use the ViterBrain Napari Plugin
  • License

Publication Related Code

  • Fitting Splines to Axonal Arbors Quantifies Relationship between Branch Order and Geometry
    • Publication
    • How to reproduce this experiment
  • Hidden Markov Modeling for Maximum Likelihood Neuron Reconstruction
    • Manuscript
    • How to use ViterBrain

Useful Links

  • Brainlit @ GitHub
  • Issue Tracker
brainlit
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  • Overview: module code

All modules for which code is available

  • brainlit.algorithms.connect_fragments.viterbrain
  • brainlit.algorithms.detect_somas.detect
  • brainlit.algorithms.generate_fragments.adaptive_thresh
  • brainlit.algorithms.generate_fragments.state_generation
  • brainlit.algorithms.trace_analysis.fit_spline
  • brainlit.algorithms.trace_analysis.spline_fxns
  • brainlit.feature_extraction.neighborhood
  • brainlit.preprocessing.image_process
  • brainlit.preprocessing.preprocess
  • brainlit.registration.file_io
  • brainlit.registration.transform
  • brainlit.registration.visualization
  • brainlit.utils.Neuron_trace
  • brainlit.utils.session
  • brainlit.viz.swc2voxel

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