https://doi.org/10.5061/dryad.np5hqc03s

Description of the data and file structure

Experiments in"Chronic recording of brain activity in awake toads"

The purpose of these experiments was to overcome obstacles to establish chronic electrophysiology recordings in awake toads. In order to overcome issues related to amphibian physiology and brain movement, we implemented the use of flexible mesh electronics to record activity from the telencephalon of awake toads over five days, and from an anesthetized toad over 15 weeks. This represents a far greater duration of recording than previously achieved in amphibians, and is also one of the first successful efforts to record brain activity from awake, non-paralyzed amphibians.

Files and variables

File: F02_data.zip

Description: This folder holds raw RHD files that each represent one minute of raw neural recording data from toad F02. Each minute of recording comes from a different day, indicated in the title of the RHD. Recordings in F02 were done while the animal was awake but restrained in a sling, and the flexible mesh electronics in the brain were connected by wire to an Intan RHD Data Acquisition system that uses RHX Data Acquisition software. Recordings in F02 happened over five consecutive days.

File: F03_data.zip

Description:  This folder holds raw RHD files that each represent one minute of raw neural recording data from toad F03. Each minute of recording comes from a different day, indicated in the title of the RHD. Recordings in F02 were done while the animal was awake but restrained in a sling, and the flexible mesh electronics in the brain were connected by wire to an Intan RHD Data Acquisition system that uses RHX Data Acquisition software. Recordings in F03 happened over five consecutive days.

File: M01_data.zip

Description: This folder holds raw RHD files that each represent one minute of raw neural recording data from toad M01. Each minute of recording comes from a different day, indicated in the title of the RHD. Recordings in M01 were done while the animal was lightly anesthetized and the mesh electronics in the brain were connected by wire to an Intan RHD Data Acquisitionsystem that uses RHX Data Acquisition software. Recordings happened 9 times over 15 weeks. 

File: F05_data.zip

Description: This folder holds raw RHD files that each represent one minute of raw neural recording data from toad F05. Each minute of recording comes from a different day, indicated in the title of the RHD. Recordings in F05 were done while the animal was awake and unrestrained in a clear plastic tote box, and the flexible mesh electronics in the brain were connected by wire to an Intan RHD Data Acquisition system that uses RHX Data Acquisition software. Recordings in F05 happened over five days in a seven day period.

File: F06_data.zip

Description: This folder holds raw RHD files that each represent one minute of raw neural recording data from toad F06. Each minute of recording comes from a different day, indicated in the title of the RHD. Recordings in F06 were done while the animal was awake and unrestrained in a clear plastic tote box, and the flexible mesh electronics in the brain were connected by wire to an Intan RHD Data Acquisition system that uses RHX Data Acquisition software. Recordings in F06 happened over five days in a seven day period.

File: F07_data.zip

Description: This folder holds raw RHD files that each represent one minute of raw neural recording data from toad F07. Each minute of recording comes from a different day, indicated in the title of the RHD. Recordings in F07 were done while the animal was awake and unrestrained in a clear plastic tote box, and the flexible mesh electronics in the brain were connected by wire to an Intan RHD Data Acquisition system that uses RHX Data Acquisition software. Recordings in F07 happened over 5 consecutive days.

Code/software

Matlab Scripts for Visualizing Data

To process this data for spike sorting, we used a number of Matlab scripts that we have uploaded as well. Here are brief descriptions of the scripts:

spike_sorter_core_submission.m - This script allows you to set the parameters of spike sorting. It references read_Intan_512RHD_no_prompt.m, which can be dowloaded from the Intan website. 

The following parameters can be manipulated:

- startSortingTime and endSortingTime: allows you to pick a time range (in seconds) in a recording file to consider for spike sorting

- channels- allows you to select which channels to sort

- Time and amplitude constraints:

-pre/post spike durations

-detectMode: allows you to select “positive” peaks, “negative” peaks, or “both”

-thresholdSetValue: allows you to set an amplitude value (in microvolts) that spikes must exceed to be sorted

-artifactCutoff: Maximum amplitude for artifact removal in microvolts

-Bandpass filter parameters

-samplerate - 20000 Hz for all recordings in this experiment

-passBand - allows you to select frequency band; 250-6000 Hz for this experiment

spike_sorter_submission.m - This is the script you run to perform spike sorting, and it references the spike_sorter_core_submission.m script.  You can change the plotting parameters in this script. Daniel Shaykevich adjusted this script with the help of chatGPT, to plot mean waveforms with standard deviation shading, and checked the work to confirm it was accurate. Currently outputs filtered traces of sorted channels with peak indicators marking spike locations, a plot with all individual sorted waveforms overlayed on each other,  a plot of mean waveform of sorted spikes with standard deviation shading, and the raw traces from all filtered channels. 

ISI_log.m - This script plots the inter-spike interval histograms of sorted channels using the Spike_Locations.dat file output by running spike_sorter_submission.m. Daniel Shaykevich adjusted this script with the help of chatGPT to plot ISIs on a logarithmic time scale. 

Change Log

March 2025: Raw data from three additional experimental subjects have been added