Download neo4j-3.2.1 from the zip or tar file, not the exe or dmg.
Untar/unzip it into a directory of your choice, let say, "myneo4j"
Setup the tools required for exporting to other formats, go to neo4j-shell-tools and download the "neo4j-shell-tools_3.0.1.zip" file.
Unzip neo4j-shell-tools.zip and copy the 4 jar files into your "myneo4j/lib" directory.
Setup your path variables,
e.g. macOS
export NEO4J_HOME=/Users/yourname/myneo4j/neo4j-community-3.2.1
export PATH=$PATH:$NEO4J_HOME/bin:$NEO4J_HOME/lib
This makes the neo4j-shell-tools available.
Now generate a neo4j graph database from your Stix objects file using StixToNeoDB
java -jar stixtoneodb-6.0.jar --json stix_file.json stixdb
This will produce a neo4j database in the "stixdb" directory.
After that, in a terminal type:
neo4j-shell -path /path_to.../stixdb
Then for example exporting to graphML format, type at the shell prompt:
$ export-graphml -o out.graphml
This will give you all your data in graphML format, you can then open "out.graphml" using Gephi.
Other export commands are available,
To export your data as Cypher statements, use the Cypher Export command.
To export your data as CSV, use the Cypher Import command with the -o file option which will output the results of your queries into a CSV file.
To export your data as GraphML, use the GraphML Export command.
To export your data as a binary file, use the Export Binary command.