From 6ddce352a2feab829a16c7ceb89eaa5a9d396fe0 Mon Sep 17 00:00:00 2001 From: William Silversmith Date: Wed, 31 Jan 2024 17:34:51 -0500 Subject: [PATCH] docs: show how to use the cross sectional area computation --- README.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 1a8da079..58aedeb7 100755 --- a/README.md +++ b/README.md @@ -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 @@ -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)