AxIS Data in Spotfire - Axion BioSystems · Axion BioSystems AxIS Data in Spotfire 7 third column (Dose) ... the y-axis to “Electrode Number” by selecting it from the drop-down

Axion BioSystems AxIS Data in Spotfire 1

AxIS Data in Spotfire

1. Objective

Spotfire is a data visualization and manipulation tool that can be used to analyze spike and beat

data collected using AxIS. This document describes the steps necessary to (1) import AxIS data

files into Spotfire, (2) extract channel and well identifiers, (3) combine data from multiple files,

and, (4) generate basic visualizations, such as raster plots.

2. Importing Data

Spotfire can import spike- or beat-list files generated by AxIS. These are files with a “.csv”

extension (comma-separated variable) containing a chronological list of the time a Spike or

Beat occurred, the electrode where it was located, and associated waveform measurements.

These outputs are generated using the neuronal Spike Detector or cardiac Beat Detector

processing elements respectively. Load this data into Spotfire by clicking File Add Data

Tables.

In the Add Data Tables pane, click Add, and choose Files from the dropdown menu.

Figure 1. Select AxIS file in the Add Data Tables pane.

Navigate to the appropriate directory and select the AxIS file that contains the desired data. A

preview of the imported data will appear (Fig. 2 below). Use this preview tool to select which

columns to include. For the spike list data shown below, the first two columns contain “header”

information about acquisition and analysis and are not needed for the spike analysis. Deselect

these columns and choose OK.

Add data from AxIS file


Figure 2. Preview of the imported data from an AxIS spike list file. Use the checkboxes above each column to select which columns to include in the Spotfire data table.

Now, click OK in the Add Data Tables dialog box and a default bar chart will be plotted. Close

this chart using the close icon that appears when the mouse is scrolled over the upper right

corner of the Bar Chart panel. Select Insert New Visualization Table to see the imported

data (Fig. 3).

Figure 3. Imported data from AxIS spike list file.

Columns to include


3. Extract Channel and Well Identifiers

It is usually important to sort the data by well and electrode. To sort this way, the Electrode

column must be separated into two columns, one with the Well Number and one with the

Electrode Number.

3.1 Create a Well Number Column

Click Insert Calculated Column. In the Expression box, type:

Mid([Electrode],1,(Find("_",[Electrode])-1))

(Fig 4). This will search for the underscore between the well number and the electrode number,

and put the well number into a new column. At the bottom of the window, type “Well Number”

into Column name and click OK.

Figure 4. Create new columns based on data in existing columns by creating a calculated column.

To display the new column, right click on the data table and select Properties. Click on Columns

on the left and add Well Number to Selected columns (Fig. 5).

Expression

Column name


Figure 5. Use the data table Properties pane to display the newly created column.

3.2 Create an Electrode Number Column

Repeat this procedure to create a new column containing the Electrode Number by clicking on

Insert Calculated Column. In the Expression box, type:

Mid([Electrode],(Find("_",[Electrode])+1),Len([Electrode]))

Type “Electrode Number” into Column name and click OK (Fig. 4). To display this column in the

data table, add it using the data table Properties pane (Fig. 5).

3.3 Delete the Concatenated Electrode Column

Confirm that the Well Number and Electrode Number were correctly extracted from the

combined well and electrode information in the Electrode column. Remove the Electrode

column by clicking Edit Column Properties. Choose “Electrode” from the list of Column

names and click Delete. Then click OK, and the column will be removed from the data table

(Fig. 6).

Select columns

Columns to display in table

Select columns


Figure 6. Delete selected columns using the Column Properties pane.

4. Combine Data Tables

Combining data from multiple tables can be useful. For example, the above data table contains

spike information according to the well and electrode number. Combining AxIS-generated data

with a plate map makes it possible to manage data according to the compounds applied. Use

Excel to create a file with a well map that specifies the compound and concentration added to

each well (Table 1).

1 2 3 4 5 6 7 8

A 10mM TEA 0.3mM

TEA 3mM TEA 3uM GABA

30uM GABA

300uM GABA

NMM Control

B 0.3mM


30uM GABA

300uM GABA

NMM Control

C 10mM TEA 0.3mM


30uM GABA

300uM GABA

NMM 10uM

GABAzine

D 10mM TEA 16.7uM

Lido

2uM GABAzine

2uM GABAzine

2uM GABAzine

E 16.7uM

Lido 50uM Lido

150uM Lido

150uM Lido

10uM GABAzine

10uM GABAzine

F 16.7uM

Lido 50uM Lido 50uM Lido

150uM Lido

Table 1. Excel table containing dosing information.

4.1 Load the Dosage Data into Spotfire

To combine this data with the previously loaded spike list data, first load the dosage data into

Spotfire. Click File Add Data Tables. Click Add, and choose Files from the dropdown menu.

Select the file that contains the dosing information. Use the preview to verify that the top row of

the well map (well column numbers 1-8) was imported as the column names, and click OK (Fig.

7). If the well column numbers 1-8 are imported as the first row of data instead of the column

Delete Column to delete


names, select Name row from the drop-down menu under Type, and click OK to return to the

Add Data Tables pane.

Figure 7. Preview of the imported data. Verify the column names were assigned properly.

4.2 Rearrange the Table into Columns

In the dropdown menu under Transformations, select Unpivot and click Add.

Figure 8. Use the Add Data Tables pane to rearrange the data into columns.

Add “Column 1” to Columns to pass through, and Add columns 1-8 to Columns to transform

(Fig. 9). Type “WellCol” for Category column name and “Dose” for Value column name. In the

sample pane at the bottom, the data should now be organized such that the first column

(Column 1) is the Well Row (A-F), the second column (WellCol) is the Well Column (1-8) and

Row type

Transformation Add Unpivot

Verify column names


third column (Dose) is the compound applied to each well. Click OK to return to the Add Data

Tables pane.

Figure 9. Use the Unpivot Data pane to specify which columns to transform.

4.3 Combine Columns:

Combine the Well Row (Column 1) and Well Column (WellCol) to create a new column called

Well Number that matches the column created in the previous data table. In the dropdown menu

under Transformations, select Calculate New Column and click Add (Fig. 8). In the Calculate

New Column pane, type:

Concatenate([Column 1],[WellCol])

into the Expression Box, and type “Well Number” into Column name, then press OK (see Fig 4).

In the Add Data Tables pane, 1. Unpivot and 2. Calculated Column should be listed in the

Transformations box (Fig. 10). Click OK.

Column names

Pass Column 1

Transform 1-8


Figure 10. Add Data Tables pane showing the Excel dosing table and the two transformations.

4.4 View Table to Verify Data Loaded Properly:

Close the default bar chart that pops up on page 2, and view the data table by clicking on Insert

New Visualization Table. This creates a table displaying the spike data, not the dosing

information data just loaded. To display the dosing information table, click on the Data table:

drop-down menu on the far right of the plot window, and select the dosing information data.

4.5 Combine Data Tables:

To add this dosing information to the table containing the spike information, click Insert

Columns.

In the dropdown menu, select the first table created, “Spike_List_Neural_DemoData” in this

example, as the destination table and click Next.

In the Insert Columns – Select Source pane, under Add columns from, select “Existing data

table in my analysis” (Fig. 11). Click Browse and select the second data table, in this example

“Sample_Dosing_Layout”.

Transformations


Figure 11. Select the source to add columns from in the Insert Columns pane.

No transformations are necessary, so click Next. In the Match Columns pane, click Match All

Possible and “Well Number” will appear under Matched columns (Fig. 12). Click Next, and

check the box beside “Dose” to add this column of dosing information to the data table. Then

click Finish.

Figure 12. In the Match Columns pane, specify the columns to match between the two data tables, and in the Import pane, specify the columns from the second data table to be added to the first data table.

To view the combined data table (Fig. 13), return to the spike information data table, and right-

click to select Properties, then Add “Dose” to Selected columns.

Existing data


Figure 13. Combined data table containing both spike and dosing information.

It is also possible to create separate columns for drug names and concentrations. To do this,

split the “Dose” column into two columns by searching for the space between the drug

concentration and name, using the steps outlined in section 3.


5. Neural Application: Raster Plot

MEA data is often visualized using raster plots, which present a hash mark for each spike event

in time, across all electrodes in a well. To generate a raster plot, select Insert New

Visualization Scatterplot.

The default x-axis is “Time”, which is correct, however the default y-axis is “Amplitude”. Change

the y-axis to “Electrode Number” by selecting it from the drop-down menu on the y-axis label

(Fig. 14).

Figure 14. Select Electrode Number from the drop-down menu on the y-axis.

5.1 Change the Marker Shape:

The default marker shape is a square, but for a raster plot a small vertical line marking the exact

spike time is more effective. To change the marker shape, right-click on the scatterplot and

select Properties. Choose Shape from the menu on the left, and then in the drop-down menu

under Shape, select the vertical line (Fig. 15), and close the Properties pane.

Figure 15. Use the Properties pane to make modifications to the plot appearance.

y-axis selection


5.2 Use Filters to Plot Specific Wells:

The filters on the far right side of the plot make it possible to limit the raster plot to a subset of

wells. This might include a single well (Fig. 16), or all wells that received the same treatment

(Fig. 17).

Figure 16. Raster plot showing all spikes in well A6.

Figure 17. Raster plot showing all spikes in wells treated with 0.3mM TEA. Well A2 spikes are blue, B2 spikes are yellow, and C2 spikes are pink. To group the spikes according to well as shown here, first select Well Number in the y-axis drop-down menu. Then click the + beside Well Number to add an additional y-axis, and select Electrode Number from that drop-down menu.

Filter options


6. Cardiac Application: BPM Plot

When examining cardiac data, it is useful to look at the beat rate across wells, measured in

beats per minute (bpm). In a new Spotfire project file, load a cardiac beat list csv file generated

by AxIS into Spotfire using the procedure described in section 2. Separate the Electrode column

into Well Number and Electrode Number, as described in section 3, and join the data with

dosing information if desired (section 4).

6.1 Calculate and Plot BPM:

The cardiac beat list file includes the beat period for each beat. Instantaneous BPM can be

computed using the expression: BPM=60sec/beat period. Choose Insert Calculated Column,

and type:

60/[Beat Period (s)]

into the Expression box and BPM into the Column name and click OK. To plot the average BPM

(across all channels and all beats in each well) for all wells, choose Insert New Visualization

Bar Chart and select Well Number from the drop-down menu on the x-axis. Select BPM from

the drop-down menu on the y-axis, and choose Avg() from the drop-down menu at the top of the

y-axis selection pane in order to plot Avg(BPM) (Fig. 18).

Figure 18. Bar plot showing BPM in all wells. Specify which data to plot using the drop-down menu on the y-axis. Specify the independent variable of interest using the drop-down menu on the x-axis.

To add error bars, right-click on the bar plot and select Properties, then select Error Bars in the

list on the left side of the Bar Chart Properties pane. In the Upper Error: and Lower Error: drop-

down menus, specify error bars of size StdDev(BPM) by selecting StdDev from the drop-down

at the top and BPM from the list of columns (Fig. 19).

This technique can also be used to plot the BPM for all treatments performed, by choosing Dose

on the x-axis.


Figure 19. Use the Bar Chart Properties pane to display error bars on the bar plot.


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AxIS Data in Spotfire - Axion BioSystems · Axion BioSystems AxIS Data in Spotfire 7 third column (Dose) ... the y-axis to “Electrode Number” by selecting it from the drop-down