Freshly recorded raw data generally needs to go through a number of preprocessing and annotation steps before it is ready to be analyzed. Especially when setting up a new task and/or drive layout, annotation can take a lot of time. If you want to extract spike trains, you will need to spike sort the raw data, which depending on the number of recording sites and the quality of your data can take up to 2 hours per tetrode.

Raw data should immediately be uploaded to the Incoming folder on the lab database, and backed up to a secondary location such as on your own computer or to DVD.

When preprocessing is complete, the resulting set of files moves to the Promoted folder. When you promote your first data sets, ask MvdM to verify accuracy and completeness.

We use two different data acquisition systems in the lab. Raw data from a recording session using the Neuralynx system consists of the following files:

• *.Ncs files: continuously sampled data, “local field potentials”
• *.ntt files: raw tetrode files (or *.nst, stereotrode files)
• *.Nev file: raw Events file
• *.Nvt file: video tracking file (usually zipped to save space)

For most tasks, when promotion is complete the following files are also available: The following files are the result of preprocessing and annotation:

• *.t files: spike times for one putative neuron (output from MClust, a spike sorting program)
• *.clusters: cluster information (output from MClust, you will generally not need this)
• *wv.mat and *ClusterQual.mat files: waveforms and cluster quality metrics
• *Metadata.mat file: structured task-related information such as locations of feeders, times of rewards, etc. (not included in all sessions)
• *ExpKeys.m file: basic information about this recording session, such as task, start time, end time, etc. (note this is a .m file, so needs to be run rather than loaded as you would a .mat file)
• *vt.mat file: pre-processed video tracking data

Note the naming convention for the above files: all files are identified by the RYYYY-MM-DD string in the filename, and recording files are further named with the tetrode number.