We use light-sheet microscopy in behaving larval zebrafish to monitor neural responses across the entire nervous system, at single-cell resolution.
This website is a companion to these papers
The examples highlight how these technologies can be used to find patterns in large-scale brain activity.
Most modern computers with Python 2.7 should be able to get started in just a few steps. (If you aren't already using Python, start by getting Anaconda.)
1. Download the latest, pre-built version of Spark, and set one environmental variable
$ export SPARK_HOME=</your/path/to/spark>
2. Type this into the terminal
$ pip install thunder-python
3. Set up an Amazon account and credentials (see instructions), then start a cluster
$ thunder-ec2 -i mykey -k mykey.pem -s 5 launch test
4. Login to the cluster, start thunder, and load an example data set
$ thunder-ec2 -i mykey -k mykey.pem -s 5 login test $ thunder >> data, params = tsc.loadExampleEC2('zebrafish-optomotor-response')
For detailed instructions, read the documentation: