Neuron Data Browser Transform API

Service to transform Janelia to Allen coordinates using registration files.

Build Notes

This references a forked version of hdf5.node that is customized to

• allow getting the dimensions and contents of 4-D datasets
• perform multiple reads from a single file open

This was forked when nodejs 8.12 was the latest stable release. yarn install will fail with newer versions of nodejs.

Reading HDF5 files will need to be updated (e.g., reapply above additions to the latest hdf5.node) to build or run with a newer nodejs version.

Tools

Reapply all transforms (using registration used for previous transform).

docker run -it --rm --network mnb_back_tier -e DATABASE_PW=${DATABASE_PW} -v ${TRANSFORM_VOL_EXT}:${TRANSFORM_VOL_INT}  mouselightdatabrowser/transform-api:1.6 /bin/bash

export DEBUG=mnb:*
export export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/usr/local/lib

API Usage

Full Swc Tracing Query

{
  swcTracings {
    id
    filename
    annotator
    fileComments
    offsetX
    offsetY
    offsetZ
    firstNode {
      id
      sampleNumber
      parentNumber
      x
      y
      z
      radius
      structureIdentifier {
        id
        name
        value
        mutable
        createdAt
        updatedAt
      }
    }
    tracingStructure {
      id
      name
      value
      createdAt
      updatedAt
    }
    createdAt
    updatedAt
  }
}

#####Full Tracing Query

{
  tracings {
    id
    nodeCount
    transformedAt
    createdAt
    updatedAt
    transformStatus {
      startedAt
      inputNodeCount
      outputNodeCount
    }
    firstNode {
      id
      sampleNumber
      parentNumber
      x
      y
      z
      radius
      structureIdentifier {
        id
        name
        value
        mutable
        createdAt
        updatedAt
      }
    }
    swcTracing {
      id
      filename
      annotator
      fileComments
      offsetX
      offsetY
      offsetZ
      firstNode {
        id
        sampleNumber
        parentNumber
        x
        y
        z
        radius
        structureIdentifier {
          id
          name
          value
          mutable
          createdAt
          updatedAt
        }
      }
      tracingStructure {
        id
        name
        value
        createdAt
        updatedAt
      }
      createdAt
      updatedAt
    }
    registrationTransform {
      id
      name
      location
      notes
      createdAt
      updatedAt
    }
    tracingStructure {
      id
      name
      value
      createdAt
      updatedAt
    }
  }
}

#####Apply Transform

mutation {
  applyTransform(swcId: "7d4af5fd-e121-4425-9143-a166d8c94fa6") {
    id
    transformedAt
    nodeCount
    firstNode {
      id
    }
    swcTracing {
      id
    }
    registrationTransform {
      id
      name
      location
      notes
    }
    tracingStructure {
      id
      name
      value
    }
    transformStatus {
      startedAt
      inputNodeCount
      outputNodeCount
    }
    createdAt
    updatedAt
  }
}