Data Instances

The Hemibrain databases include many data instances necessary for the FlyEM Team's reconstruction of the dataset. The most useful data are described below. To interact with a data instance through the HTTP API, look at its documentation by either clicking on its label type in the DVID console or using a URL like http://localhost:8000/api/help/labelmap where localhost:8000 is the main DVID server and labelmap is the data type of the instance you are trying to query.

Data InstanceData TypeDescription
bookmark_annotationsannotationGeneral user-tagged point annotations
segmentation_todoannotationTo-do annotations for organizing proofreading workflow
synapsesannotationThe synapse data organized spatially, by tag, and by label.
roisSmoothedDecimatedkeyvalueKey = ROI name.Value = Smoothed, decimated ROI surface mesh.
segmentation_annotationskeyvalueSee Note 1.
segmentation_mesheskeyvalueKey = label ID + ".ngmesh". Value = Neuroglancer mesh.
segmentation_skeletonskeyvalueKey = label ID + "_swc". Value = SWC file.
segmentationlabelmapThe supervoxel and agglomerated label of every voxel.
segmentation_roi_voxelslabelmapSee Note 2.
synapses_labelszlabelszSee Note 3.
AB(L) to vACA(R)roiEach ROI is composed of run-length encoded spans of 32^3 voxel blocks.


  1. Labeled neurons can have a number of properties like class/instance (name is deprecated), status, and comment.
  2. Each voxel in segmentation_roi_voxels has a label corresponding to its position in a list of ROIs, where the label 1 is for AB(L), label 2 is for AB(R), etc. The list of ROIs: ["AB(L)", "AB(R)", "AL(L)", "AL(R)", "AME(R)", "AOTU(R)", "ATL(L)", "ATL(R)", "AVLP(R)", "BU(L)", "BU(R)", "CA(L)", "CA(R)", "CAN(R)", "CRE(L)", "CRE(R)", "EB", "EPA(L)", "EPA(R)", "FB", "FLA(R)", "GNG", "GOR(L)", "GOR(R)", "IB", "ICL(L)", "ICL(R)", "IPS(R)", "LAL(L)", "LAL(R)", "LH(R)", "LO(R)", "LOP(R)", "ME(R)", "NO", "PB", "PED(R)", "PLP(R)", "PRW", "PVLP(R)", "SAD", "SCL(L)", "SCL(R)", "SIP(L)", "SIP(R)", "SLP(R)", "SMP(L)", "SMP(R)", "SPS(L)", "SPS(R)", "VES(L)", "VES(R)", "WED(R)", "a'L(L)", "a'L(R)", "aL(L)", "aL(R)", "b'L(L)", "b'L(R)", "bL(L)", "bL(R)", "gL(L)", "gL(R)"].
  3. Index of labels sorted by number of synapses by type: PostSyn (post-synaptic), PreSyn (pre-synaptic), etc.