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docs: show how to use the cross sectional area computation
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william-silversmith committed Jan 31, 2024
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Expand Up @@ -467,7 +467,9 @@ Of note: Meshing is a memory intensive operation. The underlying zmesh library h
Igneous provides the engine for performing out-of-core skeletonization of labeled images.
The in-core part of the algorithm is provided by the [Kimimaro](https://github.com/seung-lab/kimimaro) library.

The strategy is to apply Kimimaro mass skeletonization to 1 voxel overlapping chunks of the segmentation and then fuse them in a second pass. Both sharded and unsharded formats are supported. For very large datasets, note that sharded runs better on a local cluster as it can make use of `mmap`.
The strategy is to apply Kimimaro mass skeletonization to 1 voxel overlapping chunks of the segmentation and then fuse them in a second pass. Both sharded and unsharded formats are supported. For very large datasets, note that sharded runs better on a local cluster as it can make use of `mmap`.

We also support computing the cross sectional area at each vertex, but be aware that this will add significant time to the computation (currently many hours for a densely labeled task). This is practical for sparse labeling though. This should be improved substantially in the future.

#### CLI Skeletonization

Expand Down Expand Up @@ -513,6 +515,8 @@ tasks = tc.create_skeletonizing_tasks(
parallel=1, # Number of parallel processes to use (more useful locally)
spatial_index=True, # generate a spatial index for querying skeletons by bounding box
sharded=False, # generate intermediate shard fragments for later processing into sharded format
cross_sectional_area=False, # Compute the cross sectional area for each vertex.
cross_sectional_area_smoothing_window=5, # Rolling average of vertices.
)

# Second Pass: Fuse Skeletons (unsharded version)
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