ClearMap Documentation¶
- Overview
- Installation
- Functionality
- Usage
- WobblyStitcher
- CellMap
- CellMap Tutorial
- TubeMap
- Pipeline
- Clipping, masking and first binarization
- Light-sheet artifact correction
- Median filter
- Pseudo deconvolution and second binarization
- Adaptive threshold and third binarization
- Equalization and fourth binarization
- Tube filtering and fifth binarization
- Binary filling
- Deep Vessel Filling
- Binary smoothing
- Skeletonization and graph construction
- Vasculature graph geometry extraction
- Vasculature vertex and branch labeling
- Vasculature graph atlas annotation
- Pipeline
- TubeMap Tutorial
- News and Media
ClearMap API¶
- ClearMap
- Alignment
- Analysis
- Compile
- Environment
- External
- IO
- ImageProcessing
- ParallelProcessing
- Scripts
- Settings
- Tests
- Utils
- Visualization