This package is designed to work with data generated the by the Intan RHA/RHD series acquisition boards in MATLAB. The typical usage scenario is to run this script in MATLAB as a daemon to process files generated by the RHA or RHD acquisition systems. As files are generated, the software automatically extracts "relevant" data and discards "irrelevant" data. In Tim Gardner's lab, we use the software to only extract electrophysiology recorded during zebra finch vocalizations. Some other uses include extracting data aligned to stimulus playback.

The input is RHA/RHD acquisition board-generated data, and the output is automatically organized files read to be analyzed in MATLAB. It should be noted that using this toolbox requires a passing familiarity with MATLAB, as it is command window oriented (i.e. no pretty GUI).

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1. Requirements
2. Data types
3. Directories
4. Conventions
5. Data extraction
6. Extracted data structure
7. Filename Options
8. Script Options

###Requirements

This has been tested using MATLAB 2010A and later on Windows and Mac (Linux should be fine). You must have the markolab and zftftb toolboxes in your MATLAB path. The only MATLAB Toolbox required is the Signal Processing toolbox.

###Data types

So far the two data types that are guaranteed to work are files generated by the Intan RHA/RHD acquisition systems, which generated *.int and *.rnd files, respectively. The software can be extended to work with other file types, and Open Ephys is already in the works.

###Directories

First you need to create the following five directories:

/WHERE_I_STORE_DATA/staging/
/WHERE_I_STORE_DATA/staging/processed/
/WHERE_I_STORE_DATA/staging/unprocessed/
/WHERE_I_STORE_DATA/staging/unorganized/
/WHERE_I_STORE_DATA/intan_data/

Note that these can all be automatically generated using the script intan_frontend_mkdirs.m

All of these directories can be customized (see script options).

###Conventions

By default, the software will attempt to parse metadata about your recording from the filename itself. This means that proper data extraction requires appropriate naming conventions. The only two required specifications are the ANIMAL ID and RECORDING ID. More precisely:

[ANIMALID]_[RECORDINGID]_[OPTION1]_[OPTION2]_[TIMESTAMP]

Underscore _ is the default delimiter, but this can be changed in the script options. The timestamp is automatically appended by the Intan acquisition software, so you are only responsible for the other options. An example base filename (i.e. without the timestamp) is:

lb119_LeftHVC_mic1adc_playback3adc

This means that the animal ID is lb119 the recording ID is LeftHVC and the final two options specify where task-relevant data can be found (more on these [here] (#filename-options)). The extracted data will be placed in:

intan_data/lb119/LeftHVC/YYYY-MM-DD

Where YYYY-MM-DD is the datestamp for the data (e.g. 2014-02-13).

###Data Extraction

When "relevant" data is found, it is extracted into the /intan_data/ directory with the following structure by default:

/ANIMAL_ID/RECORDING_ID/YYYY-MM-DD

Sub-directories of this directory contain different data types:

If the task is based on TTL signals or playback this will be appended to the basic sub-directory names for clarity, e.g. gif_playback would contain spectrograms of stimuli played to the animal, or mat_ttl would contain data aligned to TTL signals.

###Extracted Data Structure

Data contained in the gif and wav directories should be self-explanatory. The MATLAB files in the mat directory contain the following variables:

###Filename Options

Many relevant options can be specified in the base filename itself. If they are not specified, they can be passed using the script option parse_options (see script options for more details). Recall the format:

[ANIMALID]_[RECORDINGID]_[OPTION1]_[OPTION2]_[OPTIONX]

These options can be broken down into specifying the data type, source (RHD only), channel, and port (RHD only). The data type can be:

This is followed by the channel then the source. Note that the channel can contain ranges indicated using a hyphen (e.g. 4-8 expands to 4,5,6,7,8) and multiple channels can be specified using any symbol other than the field_delimiter or bird_delimiter (e.g. 4-8+10 expands to 4,5,6,7,8,10 and 4-8+12-15+17 to 4,5,6,7,8,12,13,14,15,17). The data source can be (relevant only for RHD system):

So to indicate that you're recording audio data on ADC-0 and playback data on ADC-1 with animal LDR4 with recording ID NCM:

LD4_NCM_mic0adc_playback1adc

By default, audio and playback data will be saved in the MATLAB files, while spectrograms and wav files will only contain the audio data from ADC-0 (the script can generate spectrograms and wav files for the playback data by specifying script options).

Also, multiple animals can be specified using the bird_delimiter (see script options). For instance:

LD4_NCM_mic0adc_playback1adc&rm7_HVC_mic2adc_ttl4digin

This base filename would specify that animal ID 1 is LD4 recording ID 2 is NCM, animal ID 2 is rm7 and recording ID 2 is HVC. The various options specify where audio, playback, or TTL signals reside.

###Script Options

There are lots and lots of options to specify how things run "under-the-hood", e.g. the spectrogram parameters, sensitivity of vocalization detection, what directories to use, etc. All options are specified using parameter/value pairs (examples are given below the table). Here's the full list, organized thematically: