Local Configuration

NeuTu can be configured to connect to external services, list default databases, and define behaviors for certain databases.

Settings Dialog

Global Settings Dialog

Config File

This field points to the path of the configuration file for general proofreading settings and predefined databases. The file is supposed to be a JSON file contain a JSON object. Some important fields in the JSON object include:

  • "librarian": address of the default librarian;

  • "neutu_server": address of the default neutuse server (https://github.com/janelia-flyem/neutuse), which should have the pattern like neutuse:http://<address>;

  • "neuroglancer server": address of the default neuroglancer server;

  • "cleave server": address of the server for body cleaving (https://github.com/janelia-flyem/neuclease);

  • "dvid repo": an array of predefined DVID database settings, each itself being a JSON object. A brief schema of such an object can be seen below (if "user_name "is not specified, every user can see the settings):

JSON schema for dvid repo entry
{
"$schema": "http://json-schema.org/draft-04/schema#",
"type": "object",
"properties": {
"name": {
"description": "name of the database setting",
"type": "string"
},
"address": {
"description": "host address of the DVID database",
"type": "string"
},
"port": {
"description": "port of the database",
"type": "integer"
},
"uuid": {
"description": "uuid of the DVID repo",
"type": "string"
},
"segmentation": {
"description": "name of the segmentation data",
"type": "string"
},
"grayscale": {
"description": "name of the grayscale data",
"type": "string"
},
"comment": {
"description": "comment of the database",
"type": "string"
},
"user_name": {
"description": "who can see this database setting",
"type": "array",
"items": [
{
"type": "string"
}
]
}
},
"required": [
"address",
"port",
"uuid",
]
}
sample flyem_config.json
{
"librarian": "emdata4.int.janelia.org:9100",
"neutu_server": "neutuse:http://emdata2.int.janelia.org:2018",
"neuroglancer server": "localhost:8080",
"dvid repo": [
{
"name": "#profile#",
"address": "emdata2.int.janelia.org",
"port": 7000,
"uuid": "7abe",
"segmentation": "segmentation2",
"grayscale": "grayscale",
"comment": "2d merge"
},
{
"address": "hackathon.janelia.org",
"uuid": "2a31",
"name": "FIB25-Hackathon",
"segmentation": "segmentation",
"grayscale": "grayscale",
"comment": "FIB-25 export for hackathon",
"user_name": ["user1", "user2"]
}
}

To specify a config file while launching NeuTu (same for Neu3), you can use the --load command argument. For example:

neutu --load <config_path>

where config_path is the path of the top-level config file, in which the candidate paths of flyem config file mentioned above can be added, such as

{ "flyem": ["../local_flyem_config.json", "flyem_config.json"] }

NeuTu will try to find the default config file in the order of the array.

Remote Service

This points to remote computing services. Currently only the skeletonization service is available. You can follow the instructions from https://github.com/janelia-flyem/neutuse to set up the service. The service text should become green once you apply the settings, or it means the service is not run or connected properly.

Task Server

It sets the server for offline tasks. This one can be ignored.

Center Cut

These numbers control the size of the high-res patch at the center of the 2D view for grayscale and segmentation data.