Neuronexus EEG Probe Mapping

vhtp
mouse
EEG
Neuronexus
probe
mapping
Author

Ernie Pedapati

Published

July 7, 2023

Overview

For alignment, here are the exact description of the equipment we are using from our purchase order:

List of Materials

This protocol describes how to map the location of the Mouse EEG v2 H32 Probe with the OM Amplifier Adapter. For better or worse, like all custom probes mapping must be confirmed manually.

Probe Layout

Layout of Mouse probe from Neuronexus

This image is from the “bottom up” so the reference electrode is actually on the bottom left following implantation:

in vivo image of implanted probe

Per Neuronexus the recordings are stored in the following format:

Radiens saves primary time-series data sets (e.g., neural recordings) in a simple, open format. Each dataset (i.e. recording) is saved in a file set named ‘XDAT’ that consists of three files: (i) flat binary file containing the matrix of all sample values (typical in uV) across the multiple channels, (ii) flat binary file containing all timestamps, (iii) json text file containing enriched metadata. link

View the raw signal data using MATLAB

A native MATLAB function is available to import the XDAT dataset. The function is available https://github.com/nzgurel/AllegoProcessing_Matlab/tree/main with an example import script here.

The raw data array can be plotted using the EEGLAB functio eegplot:

Raw Data Tracing

Here we can see that channels pri_1 and pri_31 are not connected to recording sites. As the naming index starts with 0, following import into MATLAB these will be channels indexes 1 and 32.

View and export the metata data using MATLAB

We can import metadata from the json file which contains infomation about the probe layout and recording and export it as a CSV file for further analysis.

    % MATLAB code to extract metadata from XDAT dataset

    str = fileread([xdat_filename '.xdat.json']);
    jsonData = jsondecode(str);

    % extract metadata for probe mapping
    H32Metadata = jsonData.sapiens_base.biointerface_map;

    % remove non-array fields
    H32Metadata = rmfield(H32Metadata, 'samp_freq');
    H32Metadata = rmfield(H32Metadata, 'sig_units');
    
    % save metadata as CSV
    writetable(struct2table(H32Metadata),'NeuroNexusMouseEEGv2H32_Map.csv');

For convenience, I have hosted the resulting CSV file on github for futher analysis.

Examining the Probe Metadata

We will evalute the metadata in R to more easily plot and wrangle the data. First, we will load the CSV file from github and view the first 5 rows of the metadata.

# Load CSV file from github

H32Metadata <- read_csv("https://raw.githubusercontent.com/cincibrainlab/vhtp/main/chanfiles/NeuroNexusMouseEEGv2H32_Map.csv", col_types = cols())

# View the first 10 rows of the metadata
tb1 <- H32Metadata %>%
    head(5) %>%
    kable()

Table 1: Table of XDAT dataset metadata for the Mouse EEG v2 H32 Probe.

chan_name chan_type ntv_chan_idx ntv_chan_name sys_chan_idx site_shape port absolute_idx scs_to_tcs_y site_lim_x_min site_lim_z_max site_ctr_y headstage_id site_ctr_z site_ctr_x site_ctr_tcs_x site_lim_x_max probe_id site_ctr_tcs_y site_num sensor_units scs_to_tcs_z is_audio is_audio_left is_audio_right is_selected site_lim_y_min site_lim_y_max scs_to_tcs_x site_lim_z_min dsrc_uid sensor_uid site_ctr_tcs_z color_grp_idx
pri_0 ai0 0 port_A_0 0 circle A 4 0 674.114 0 404.99961 hstg__passthrough_32 0 699.1136 0 724.114 probe__eeg_mouse_1x30 0 1 uV 0 0 0 0 1 430 380 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 2
pri_1 ai0 1 port_A_1 1 circle A 5 0 674.114 0 223.99961 hstg__passthrough_32 0 699.1136 0 724.114 probe__eeg_mouse_1x30 0 2 uV 0 0 0 0 1 249 199 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 2
pri_2 ai0 2 port_A_2 2 circle A 12 0 674.114 0 99.99961 hstg__passthrough_32 0 699.1136 0 724.114 probe__eeg_mouse_1x30 0 3 uV 0 0 0 0 1 125 75 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 3
pri_3 ai0 3 port_A_3 3 circle A 6 0 564.114 0 412.99961 hstg__passthrough_32 0 589.1136 0 614.114 probe__eeg_mouse_1x30 0 4 uV 0 0 0 0 1 438 388 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 2
pri_4 ai0 4 port_A_4 4 circle A 7 0 564.114 0 287.99961 hstg__passthrough_32 0 589.1136 0 614.114 probe__eeg_mouse_1x30 0 5 uV 0 0 0 0 1 313 263 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 2

Evaluating the Probe Metadata

The metadata hasa several curosities that suggest using caution before incorporating it into your workflow.

  1. The Murine EEG v2 H32 Probe has 30 channels, not 32 (pri_0 to pri_31), as indicated by the metadata.
  2. 2D coordinate data is provided for the first 30 channels (pri_0 to pri_29), but not the last two (pri_30 and pri_31).
  3. There is no indication that channels pri_1 and pri_31 are not connected to recording sites.

This can be seen more clearly by plotting out the channels and their coordinates on a 2d scatter plot. Indeed, this layout matches the mouse 30 lead layout above.

Metadata Plot

This suggests that the metadata has the correct layout information but has not been adjusted foe the two unconnected channels. I don’t understand why this is the case, but I wil be reaching out to Neuronexus to confirm and will post their reponse.

Tracing the Probe electrodes to the amplifier adapter

The probe is connected to the headstage using the Ometics Amplifier Adapter (NPD-36-AA-GS). This connector has 36 ports and 4 guide posts.

Amplifier Adapter

These layouts are not necessarily easy to find in one place so I have included them stiched together here:

Amplifier Adapter Pin out

The Neuronexus EEG Pin Out must be rotated to match the Amplifier Adapter Pin Out. To make it easier to visualize the matching channels, I have added red EEG channel number labels to the Amplifier Adapter Pin Out. Importantly, you can see that the Mouse 30-lead EEG leaves two channels unconnected (pri_1 and pri_31). This now clearly visible in the adapter image.

Per the documentation the internal reference electrode is connected to R1. This corresponds to the “R” pin adjacent to the “0” pin once you account for the rotation of the pin out.

Mapping the Probe to the Amplifier Adapter Stage 1

The first step is to create a simple lookup table that disregards all metadata but the amplifier pin out (pri_) and the EEG probe channels (based on the connection).

This mapping will correctly pair each EEG channel to the correct signal entering the amplifier, but will not have the correct 30 lead metadata till after we remove the unconnected channels.

mea_to_hs_map <- c(
  "E1"   = 29,
  "E2"   = 27,
  "E3"   = 25,
  "E4"   = 23,
  "E5"   = 21,
  "E6"   = 19,
  "E7"   = 17,
  "E8"   = 30,
  "E9"   = 28,
  "E10"  = 26,
  "E11"  = 24,
  "E12"  = 22,
  "E13"  = 20,
  "E14"  = 18,
  "E15"  = 16,
  "E16"  = 14,
  "E17"  = 12,
  "E18"  = 10,
  "E19"  = 8,
  "E20"  = 6,
  "E21"  = 4,
  "E22"  = 2,
  "E23"  = 0,
  "E24"  = 15,
  "E25"  = 13,
  "E26"  = 11,
  "E27"  = 9,
  "E28"  = 7,
  "E29"  = 5,
  "E30"  = 3
)

# Create a dataframe from the named list
# convert this to a dataframe
mea_to_hs_map_df <- data.frame(mea_to_hs_map) %>%
  rownames_to_column(var = "mea") %>%
  rename(hs_idx = mea_to_hs_map) %>%
  as_tibble() %>%
  mutate(headset = paste0("pri_", hs_idx)) %>%
  rename(mea_formatted_name = mea,
         og_amplifier_pin = headset,
         amplifier_index = hs_idx)
  
mea_to_hs_map_df %>% head(3) %>% kable()
mea_formatted_name amplifier_index og_amplifier_pin
E1 29 pri_29
E2 27 pri_27
E3 25 pri_25 
write_csv(mea_to_hs_map_df, "MouseEEGv2H32_Import_Stage1.csv")

The final table has the final formatted MEA channel name (E1 to E30) and the headset channel name (pri_0 to pri_29). The original index (starting with 1) is also included. We will save this file to use in MATLAB during import.

The file can be downloaded here.

We can now accurately map which MEA channels correspond to which amplifier channels. The bad channels (pri_1 and pri_31) now make more sense as you can follow the mapping.

Where is the reference channel?

Reference Channel Info

As of now, we cannot find data for the reference channel (R1) either in the metadata or from the raw read of the signal data. We will need to reach out to Neuronexus to confirm location of reference channel. Since the reference channel can either by an external wire or an internal channel determined by a physical jumper wire, we would not expect the metadata to contain this information inherently. However, the actual signal data should be present.

Neuronexus Wiring Information

Mapping the Probe to the Amplifier Adapter Stage 2

Now that the mapping is complete, we can remove the unconnected channels and add the metadata to the mapping.

As you can see from the manual plot above, pri_0 contains the correct metadata for electrode E1. However, in actuality E1 data is routed through pri_29.

Alt text

Thus, the metadata is now more accurately used as a lookup table for the probe channel and uncoupled from the amplifier channel. If we assigned the metadata for pri_29 to E1, the location would be incorrect. Let’s create a stage2 mapping that has the correct metadata (primarily coordinates) for each electrode.

# read metadata csv from github
mea_metadata <- "https://raw.githubusercontent.com/cincibrainlab/vhtp/main/chanfiles/NeuroNexusMouseEEGv2H32_Map.csv"

stage2 <- read_csv(mea_metadata, col_types = cols()) %>%
  filter(sys_chan_idx < 30) %>%
  mutate(mea_formatted_name = paste0("E", sys_chan_idx+1)) %>%
  left_join(mea_to_hs_map_df %>% select(mea_formatted_name,og_amplifier_pin), by = "mea_formatted_name") %>%
  relocate(mea_formatted_name, .after = chan_name) %>%
  relocate(og_amplifier_pin, .after = mea_formatted_name)

stage2 %>% kable()
chan_name mea_formatted_name og_amplifier_pin chan_type ntv_chan_idx ntv_chan_name sys_chan_idx site_shape port absolute_idx scs_to_tcs_y site_lim_x_min site_lim_z_max site_ctr_y headstage_id site_ctr_z site_ctr_x site_ctr_tcs_x site_lim_x_max probe_id site_ctr_tcs_y site_num sensor_units scs_to_tcs_z is_audio is_audio_left is_audio_right is_selected site_lim_y_min site_lim_y_max scs_to_tcs_x site_lim_z_min dsrc_uid sensor_uid site_ctr_tcs_z color_grp_idx
pri_0 E1 pri_29 ai0 0 port_A_0 0 circle A 4 0 674.114 0 404.99961 hstg__passthrough_32 0 699.11361 0 724.114 probe__eeg_mouse_1x30 0 1 uV 0 0 0 0 1 430 380 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 2
pri_1 E2 pri_27 ai0 1 port_A_1 1 circle A 5 0 674.114 0 223.99961 hstg__passthrough_32 0 699.11361 0 724.114 probe__eeg_mouse_1x30 0 2 uV 0 0 0 0 1 249 199 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 2
pri_2 E3 pri_25 ai0 2 port_A_2 2 circle A 12 0 674.114 0 99.99961 hstg__passthrough_32 0 699.11361 0 724.114 probe__eeg_mouse_1x30 0 3 uV 0 0 0 0 1 125 75 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 3
pri_3 E4 pri_23 ai0 3 port_A_3 3 circle A 6 0 564.114 0 412.99961 hstg__passthrough_32 0 589.11361 0 614.114 probe__eeg_mouse_1x30 0 4 uV 0 0 0 0 1 438 388 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 2
pri_4 E5 pri_21 ai0 4 port_A_4 4 circle A 7 0 564.114 0 287.99961 hstg__passthrough_32 0 589.11361 0 614.114 probe__eeg_mouse_1x30 0 5 uV 0 0 0 0 1 313 263 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 2
pri_5 E6 pri_19 ai0 5 port_A_5 5 circle A 13 0 564.114 0 112.99961 hstg__passthrough_32 0 589.11361 0 614.114 probe__eeg_mouse_1x30 0 6 uV 0 0 0 0 1 138 88 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 3
pri_6 E7 pri_17 ai0 6 port_A_6 6 circle A 8 0 456.114 0 404.99961 hstg__passthrough_32 0 481.11361 0 506.114 probe__eeg_mouse_1x30 0 7 uV 0 0 0 0 1 430 380 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 2
pri_7 E8 pri_30 ai0 7 port_A_7 7 circle A 9 0 456.114 0 287.99961 hstg__passthrough_32 0 481.11361 0 506.114 probe__eeg_mouse_1x30 0 8 uV 0 0 0 0 1 313 263 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 2
pri_8 E9 pri_28 ai0 8 port_A_8 8 circle A 14 0 456.114 0 111.99961 hstg__passthrough_32 0 481.11361 0 506.114 probe__eeg_mouse_1x30 0 9 uV 0 0 0 0 1 137 87 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 3
pri_9 E10 pri_26 ai0 9 port_A_9 9 circle A 10 0 308.114 0 349.99961 hstg__passthrough_32 0 333.11361 0 358.114 probe__eeg_mouse_1x30 0 10 uV 0 0 0 0 1 375 325 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 2
pri_10 E11 pri_24 ai0 10 port_A_10 10 circle A 11 0 308.114 0 211.99961 hstg__passthrough_32 0 333.11361 0 358.114 probe__eeg_mouse_1x30 0 11 uV 0 0 0 0 1 237 187 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 2
pri_11 E12 pri_22 ai0 11 port_A_11 11 circle A 0 0 156.114 0 192.99961 hstg__passthrough_32 0 181.11439 0 206.114 probe__eeg_mouse_1x30 0 12 uV 0 0 0 0 1 218 168 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 1
pri_12 E13 pri_20 ai0 12 port_A_12 12 circle A 1 0 156.114 0 54.99961 hstg__passthrough_32 0 181.11439 0 206.114 probe__eeg_mouse_1x30 0 13 uV 0 0 0 0 1 80 30 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 1
pri_13 E14 pri_18 ai0 13 port_A_13 13 circle A 2 0 30.114 0 149.99961 hstg__passthrough_32 0 55.11439 0 80.114 probe__eeg_mouse_1x30 0 14 uV 0 0 0 0 1 175 125 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 1
pri_14 E15 pri_16 ai0 14 port_A_14 14 circle A 3 0 30.114 0 49.99961 hstg__passthrough_32 0 55.11439 0 80.114 probe__eeg_mouse_1x30 0 15 uV 0 0 0 0 1 75 25 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 1
pri_15 E16 pri_14 ai0 15 port_A_15 15 circle A 15 0 30.114 0 -49.99961 hstg__passthrough_32 0 55.11439 0 80.114 probe__eeg_mouse_1x30 0 16 uV 0 0 0 0 1 -25 -75 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 4
pri_16 E17 pri_12 ai0 16 port_A_16 16 circle A 16 0 30.114 0 -149.99961 hstg__passthrough_32 0 55.11439 0 80.114 probe__eeg_mouse_1x30 0 17 uV 0 0 0 0 1 -125 -175 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 4
pri_17 E18 pri_10 ai0 17 port_A_17 17 circle A 17 0 156.114 0 -54.99961 hstg__passthrough_32 0 181.11439 0 206.114 probe__eeg_mouse_1x30 0 18 uV 0 0 0 0 1 -30 -80 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 4
pri_18 E19 pri_8 ai0 18 port_A_18 18 circle A 18 0 156.114 0 -192.99961 hstg__passthrough_32 0 181.11439 0 206.114 probe__eeg_mouse_1x30 0 19 uV 0 0 0 0 1 -168 -218 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 4
pri_19 E20 pri_6 ai0 19 port_A_19 19 circle A 22 0 308.114 0 -211.99961 hstg__passthrough_32 0 333.11361 0 358.114 probe__eeg_mouse_1x30 0 20 uV 0 0 0 0 1 -187 -237 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 6
pri_20 E21 pri_4 ai0 20 port_A_20 20 circle A 23 0 308.114 0 -349.99961 hstg__passthrough_32 0 333.11361 0 358.114 probe__eeg_mouse_1x30 0 21 uV 0 0 0 0 1 -325 -375 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 6
pri_21 E22 pri_2 ai0 21 port_A_21 21 circle A 19 0 456.114 0 -111.99961 hstg__passthrough_32 0 481.11361 0 506.114 probe__eeg_mouse_1x30 0 22 uV 0 0 0 0 1 -87 -137 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 5
pri_22 E23 pri_0 ai0 22 port_A_22 22 circle A 24 0 456.114 0 -287.99961 hstg__passthrough_32 0 481.11361 0 506.114 probe__eeg_mouse_1x30 0 23 uV 0 0 0 0 1 -263 -313 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 6
pri_23 E24 pri_15 ai0 23 port_A_23 23 circle A 25 0 456.114 0 -404.99961 hstg__passthrough_32 0 481.11361 0 506.114 probe__eeg_mouse_1x30 0 24 uV 0 0 0 0 1 -380 -430 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 6
pri_24 E25 pri_13 ai0 24 port_A_24 24 circle A 20 0 564.114 0 -112.99961 hstg__passthrough_32 0 589.11361 0 614.114 probe__eeg_mouse_1x30 0 25 uV 0 0 0 0 1 -88 -138 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 5
pri_25 E26 pri_11 ai0 25 port_A_25 25 circle A 26 0 564.114 0 -287.99961 hstg__passthrough_32 0 589.11361 0 614.114 probe__eeg_mouse_1x30 0 26 uV 0 0 0 0 1 -263 -313 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 6
pri_26 E27 pri_9 ai0 26 port_A_26 26 circle A 27 0 564.114 0 -412.99961 hstg__passthrough_32 0 589.11361 0 614.114 probe__eeg_mouse_1x30 0 27 uV 0 0 0 0 1 -388 -438 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 6
pri_27 E28 pri_7 ai0 27 port_A_27 27 circle A 21 0 674.114 0 -99.99961 hstg__passthrough_32 0 699.11361 0 724.114 probe__eeg_mouse_1x30 0 28 uV 0 0 0 0 1 -75 -125 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 5
pri_28 E29 pri_5 ai0 28 port_A_28 28 circle A 28 0 674.114 0 -223.99961 hstg__passthrough_32 0 699.11361 0 724.114 probe__eeg_mouse_1x30 0 29 uV 0 0 0 0 1 -199 -249 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 6
pri_29 E30 pri_3 ai0 29 port_A_29 29 circle A 29 0 674.114 0 -404.99961 hstg__passthrough_32 0 699.11361 0 724.114 probe__eeg_mouse_1x30 0 30 uV 0 0 0 0 1 -380 -430 0 0 SmartboxPro Signals hstg__passthrough_32/probe__eeg_mouse_1x30 0 6 
write_csv(stage2, "MouseEEGv2H32_Import_Stage2.csv")

This table will be used to assign metadata to our final channel mapping and can be downloaded here.

This import process has been now incorporated into our vHTP import utility.

We’ll also post any updates from Neuronexus regarding this process and finding the reference channel.