DOI: 10.5061/dryad.np5hqc03s
title: Raw electrophysiology recording files from toads implanted with flexible mesh electronics

description: Background Amphibians represent an important evolutionary transition from
 aquatic to terrestrial environments and they display a large variety of
 complex behaviors despite a relatively simple brain. However, their brain
 activity is not as well characterized as that of many other vertebrates,
 partially due to physiological traits that have made electrophysiology
 recordings difficult to perform in awake and moving animals. New method We
 implanted flexible mesh electronics in the cane toad (Rhinella marina) and
 performed extracellular recordings in the telencephalon of anesthetized
 toads and partially restrained, awake toads over multiple days. Results We
 recorded brain activity over five consecutive days in awake toads and over
 a 15 week period in a toad that was anesthetized during recordings. We
 were able to perform spike sorting and identified single- and multi-unit
 activity in all toads. Comparison with existing methods To our knowledge,
 this is the first report of a modern method to perform electrophysiology
 in non-paralyzed toads over multiple days, though there are historical
 references to short term recordings in the past. Conclusions Implementing
 flexible mesh electronics in amphibian species will allow for advanced
 studies of the neural basis of amphibian behaviors.
description: This dataset includes RHD recording files from Intan RHD
 acquisition system and RHX software for “Chronic recording of brain
 activity in awake toads.” We have also included Matlab scripts that were
 used to process this data.  Each file in this folder is
 one minute of recording data from toad that was implanted with flexible
 mesh electronics. The toad and the date of recording is indicated in the
 filename. These are representative minutes of recording that were analyzed
 for this paper and processed with the attached Matlab scripts.
description: # Raw electrophysiology recording files from toads implanted with flexible
 mesh electronics
 [https://doi.org/10.5061/dryad.np5hqc03s](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