Connectivity analysis assumes that there is only one foreground particle and no cavities in the image. Purify locates all particles in 3D and removes all but the largest foreground and background particles, as a filtering step to prepare images for Connectivity. It is a specialised implementation of the particle-finding methods in Analyse Particles, which are designed to reduce recursion and make full use of system resources.
Odgaard A, Gundersen HJG (1993) Quantification of connectivity in cancellous bone, with special emphasis on 3-D reconstructions. Bone 14: 173-182. doi:10.1016/8756-3282(93)90245-6.
- Input
- Options
- Labelling algorithm
- Mapped: Non-recursive, memory efficient and fast.
- Multithreaded: use multiple cores and job chunking to reduce recursion. Fast on small stacks and if you have many CPU cores.
- Linear: Non-recursive but heavy on RAM and single-threaded. Fast on big stacks, but only if you have the memory.
- Chunk Size: number of slices to use in each particle labelling thread. If images are large, set this to 2
- Performance Log: Show verbose performance information to help tune your system
- Make copy: If checked, shows the result in a new window; if unchecked the result replaces the original image.
- Output
- Performance metrics (optional)
- Threads: Number of CPU cores used
- Slices: Number of slices in the input image stack
- Chunks: Number of chunks of slices, each chunk is processed independently
- Chunk size: Number of slices per chunk
- Last chunk size: size of the last chunk (the remainder chunk)
- Duration: time in seconds to complete purification
- Purified image, optionally in a new image window.
This file last modified 1345hrs 29 May 2020 © Michael Doube 2004-2026 :: Designed to be interoperable and standards-compliant.
