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Composable image chunk operators to create pipeline for distributed computation.

Project description


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  • Composable operators. The chunk operators could be freely composed in commandline for flexible usage.
  • Hybrid Cloud Distributed computation in both local and cloud computers. The task scheduling frontend and computationally heavy backend are decoupled using AWS Simple Queue Service. The computational heavy backend could be any computer with internet connection and Amazon Web Services (AWS) authentication.
  • All operations support 3D image volumes.
  • You can insert your own code as a plugin.

Image Segmentation Example

Perform Convolutional net inference to segment 3D image volume with one single command!

chunkflow read-tif --file-name path/of/image.tif -o image inference --convnet-model path/of/ --convnet-weight-path path/of/ --input-patch-size 20 256 256 --output-patch-overlap 4 64 64 --num-output-channels 3 -f pytorch --batch-size 12 --mask-output-chunk -i image -o affs write-h5 -i affs --file-name affs.h5 agglomerate --threshold 0.7 --aff-threshold-low 0.001 --aff-threshold-high 0.9999 -i affs -o seg write-tif -i seg -f seg.tif neuroglancer -c image,affs,seg -p 33333 -v 30 6 6

you can see your 3D image and segmentation directly in Neuroglancer!



After installation, You can simply type chunkflow and it will list all the operators with help message. We list the 36 available operators here. We keep adding new operators and will keep it update here. For the detailed usage, please checkout our Documentation.

Operator Name Function
agglomerate Watershed and agglomeration to segment affinity map
aggregate-skeleton-fragments Merge skeleton fragments from chunks
channel-voting Vote across channels of semantic map
cloud-watch Realtime speedometer in AWS CloudWatch
connected-components Threshold the boundary map to get a segmentation
copy-var Copy a variable to a new name
create-chunk Create a fake chunk for easy test
crop-margin Crop the margin of a chunk
cutout Cutout chunk from a local/cloud storage volume
delete-chunk Delete chunk in task to reduce RAM requirement
delete-task-in-queue Delete the task in AWS SQS queue
downsample-upload Downsample the chunk hierarchically and upload to volume
evaluate-segmentation Compare segmentation chunks
fetch-task Fetch task from AWS SQS queue one by one
generate-tasks Generate tasks one by one
inference Convolutional net inference
log-summary Summary of logs
mask Black out the chunk based on another mask chunk
mask-out-objects Mask out selected or small objects
mesh Build 3D meshes from segmentation chunk
mesh-manifest Collect mesh fragments for object
neuroglancer Visualize chunks using neuroglancer
normalize-intensity Normalize image intensity to -1:1
normalize-contrast-nkem Normalize image contrast using histograms
normalize-section-shang Normalization algorithm created by Shang
plugin Import local code as a customized operator.
quantize Quantize the affinity map
read-h5 Read HDF5 files
read-tif Read TIFF files
save Save chunk to local/cloud storage volume
save-pngs Save chunk as a serials of png files
setup-env Prepare storage infor files and produce tasks
skeletonize Create centerlines of objects in a segmentation chunk
threshold Use a threshold to segment the probability map
view Another chunk viewer in browser using CloudVolume
write-h5 Write chunk as HDF5 file
write-tif Write chunk as TIFF file


We have a paper for this repo:

  title={Chunkflow: Distributed Hybrid Cloud Processing of Large 3D Images by Convolutional Nets},
  author={Wu, Jingpeng and Silversmith, William M and Seung, H Sebastian},
  journal={arXiv preprint arXiv:1904.10489},

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