brainlit
  • Brainlit
    • Motivation
    • Installation
      • Environment
      • Install from pypi
      • Install from source
      • Common Installation Issues
    • 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
      • BrainLine: Whole-Brain Fluorescence Volume Analysis Pipeline
      • 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
    • Mapping Neurons
      • Fragment Generation
    • BrainLine
      • Data Helper Functions
      • Apply Ilastik and Validate Models
      • Results Analysis
    • Feature Extraction
      • NeighborhoodFeatures
    • Preprocessing
      • Image Processing
      • Image Filters
      • Segmentation Processing
    • 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
    • Relevant directory
    • How to reproduce this experiment
  • Hidden Markov Modeling for Maximum Likelihood Neuron Reconstruction
    • Manuscript
    • Relevant directory
    • How to use ViterBrain
  • Preserving Derivative Information while Transforming Neuronal Curves
    • Manuscript
    • Neuron Mapping
    • Poster
    • Relevant directory
    • Nyquist Sampling Rate for Projection Neuron Reconstruction
  • BrainLine: An Open Pipeline for Connectivity Analysis of Heterogeneous Whole-Brain Fluorescence Volumes
    • Publication
    • BrainLine: Whole-Brain Fluorescence Volume Analysis Pipeline

Useful Links

  • Brainlit @ GitHub
  • Issue Tracker
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