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neu-suite
neu-suite

Using them

  • Getting started
  • Cheat sheet
  • CLI reference
    • neu-vol
    • neu-morpho
    • neu-mark
    • neu-glance
    • neu-eval

API

  • API reference
    • neu_lib
      • neu_lib.frame
      • neu_lib.grid
      • neu_lib.mesh
      • neu_lib.piece
      • neu_lib.predicates
      • neu_lib.scale
      • neu_lib.skeleton
      • neu_lib.tube
      • neu_lib.vec
    • blockrun
      • blockrun.dask_config
      • blockrun.dask_runner
      • blockrun.engine
      • blockrun.manifest
    • neu_vol
      • neu_vol.aws
      • neu_vol.backends
        • neu_vol.backends.base
        • neu_vol.backends.cloudvolume
        • neu_vol.backends.dvid
        • neu_vol.backends.hdf5
        • neu_vol.backends.imagestack
        • neu_vol.backends.mapped
        • neu_vol.backends.tensorstore
        • neu_vol.backends.view
        • neu_vol.backends.webknossos
      • neu_vol.detect
      • neu_vol.dvid
      • neu_vol.location
      • neu_vol.logs
      • neu_vol.mapped
      • neu_vol.ngff
      • neu_vol.ops
        • neu_vol.ops.align
        • neu_vol.ops.convert
        • neu_vol.ops.create
        • neu_vol.ops.ingest
        • neu_vol.ops.maskvalue
        • neu_vol.ops.naming
        • neu_vol.ops.occupancy
        • neu_vol.ops.pack
        • neu_vol.ops.progress
        • neu_vol.ops.provenance
        • neu_vol.ops.rebuild
        • neu_vol.ops.relabel
        • neu_vol.ops.roi
        • neu_vol.ops.subresources
        • neu_vol.ops.wk_mappings
        • neu_vol.ops.write
      • neu_vol.piece
      • neu_vol.profiles
      • neu_vol.pyramid
      • neu_vol.readback
      • neu_vol.report
      • neu_vol.retry
      • neu_vol.scales
      • neu_vol.sharded
      • neu_vol.source_metadata
      • neu_vol.transfer
      • neu_vol.webknossos
    • neu_morpho
      • neu_morpho.allowlist
      • neu_morpho.config
      • neu_morpho.coords
      • neu_morpho.fragments
      • neu_morpho.measure
        • neu_morpho.measure.compartments
        • neu_morpho.measure.driver
        • neu_morpho.measure.metrics
        • neu_morpho.measure.paths
        • neu_morpho.measure.skeletons
        • neu_morpho.measure.sweep
        • neu_morpho.measure.tables
      • neu_morpho.mesh
      • neu_morpho.metrics_db
      • neu_morpho.occupancy
      • neu_morpho.ops
        • neu_morpho.ops.export_roi_seg
        • neu_morpho.ops.index_segments
        • neu_morpho.ops.manifest
        • neu_morpho.ops.meshify
      • neu_morpho.pipeline
      • neu_morpho.precomputed
      • neu_morpho.roi
      • neu_morpho.run_records
    • neu_mark
      • neu_mark.annotations
      • neu_mark.annsource
      • neu_mark.bodies
      • neu_mark.config
      • neu_mark.dvid
      • neu_mark.explore
      • neu_mark.io
      • neu_mark.notebook
      • neu_mark.ops
      • neu_mark.roi_layers
      • neu_mark.roi_survey
      • neu_mark.rules
      • neu_mark.segprops
      • neu_mark.tables
    • neu_glance
      • neu_glance.config
      • neu_glance.layers
      • neu_glance.movie
        • neu_glance.movie.animate
        • neu_glance.movie.rendering
      • neu_glance.served_layer
      • neu_glance.serving
      • neu_glance.shaders
      • neu_glance.sources
      • neu_glance.state
    • neu_proc
      • neu_proc.ops
        • neu_proc.ops.backend
        • neu_proc.ops.dilate
        • neu_proc.ops.dust
        • neu_proc.ops.kernels
        • neu_proc.ops.measure
        • neu_proc.ops.offset
        • neu_proc.ops.opening
    • neu_eval
      • neu_eval.adjudicate
      • neu_eval.assign
      • neu_eval.compare
      • neu_eval.disagree
      • neu_eval.overlap
      • neu_eval.tables
      • neu_eval.voxel
    • neu_draw
      • neu_draw.backends
        • neu_draw.backends.animation
        • neu_draw.backends.legend
        • neu_draw.backends.pygfx
        • neu_draw.backends.vector
      • neu_draw.cache
      • neu_draw.colors
      • neu_draw.layout
      • neu_draw.logs
      • neu_draw.orbit
      • neu_draw.scene
      • neu_draw.sources
      • neu_draw.toolbar
      • neu_draw.vectorfile
      • neu_draw.video
      • neu_draw.viewstate

Guides

  • Converting a source into a multiscale volume
  • Several small pieces into one frame
  • Reading and writing from Python
  • Ground truth: from annotated chunks to meshes
  • Viewing the results in neuroglancer
  • Rendering locally in a notebook

Tutorials

  • Synapses in neuroglancer, pre and post in two colours
  • Names and tags for a segmentation: writing a rules module

Reference

  • neu-lib
  • blockrun
  • Parallel maps with Dask + SLURM
  • neu-vol
  • neu-morpho
  • neu-mark
  • neu-glance
  • neu-draw
  • neu-proc
  • neu-eval
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neu_morpho.ops¶

High-level operations.

Submodules¶

  • neu_morpho.ops.export_roi_seg
  • neu_morpho.ops.index_segments
  • neu_morpho.ops.manifest
  • neu_morpho.ops.meshify
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neu_morpho.ops.export_roi_seg
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