Setting up a Small Animal Respirometry System: The Expedata Setup File

Of equal importance compared to a properly set up respiratory system is the configuration of a setup file to accurately acquire the data, record the data, and control key components of the system. Here we’ll configure a setup file in Expedata for the small animal respiratory system.

A quick overview of the system:

Air from the cylinder is scrubbed of CO2 and water vapor. It goes through the mass flow control valve. From the mass flow control valve, it goes into the compact baseliner, then out to the animal chamber. Air is returned to the humidity meter to measure water vapor from the animal. Then air is scrubbed of water vapor. And finally, we measure CO2 with our CO2 analyzer. Thus, we need to acquire data for CO2 in percentage, water vapor pressure, and the air flow rate. And we also need to set up digital controls for the compact base lining system and log the base line chamber switch status for the system. So, we have four data channels and a digital control profile.

First, connect a computer with Expedata installed to the UI-3 via a USB cable. Open Expedata, click on Acquire, and then click on Set Up Data Acquisition. This opens the Connect to Data Acquisition Systems window where you will connect to the UI-3. Click on Use the UI to connect to the UI-3. When you successfully connect to the UI-3, you’ll see a Connected to UI message in green. Then you can click on OK to go to the Acquisition Parameters window.

Start by setting four channels for our data acquisition. So, select four as the total number of channels, and we’ll give our channels names. Channel 1 is going to be CO2. Channel 2 will be WVP for water vapor pressure. Channel 3 is FR for flow rate. And Channel 4 will be BL for base line. These names will also later be used in macros for data analyses and extraction.

So now click on the Monitor button to verify that we have four channels and that all of them are measuring voltages between 0 and 5 volts. We have voltages, and now we want to convert these to the correct units measured by our instruments. First, check the CO2 analyzer for its analog data output range, 0 to 0.1 percent. Now select the CO2 channel and open the Transform dialog, select a linear transform, and set a multiplier of 0.02 for a B in the Equation window. Click the Monitor button again, and we see the units are units for CO2. And compare that 0.0503 with our CO2 analyzer display. Note that this matches exactly.

Now we’ll do the same thing for our water vapor channel. Make channel 2 active, and then verify the RH300 for its analog data output range, 0-2 kPa. And set our linear transform with a multiplier of 0.4, so that 5 volts is equal to 2. And again, we’ll check our monitor. The units are 0.634, and on our display, we note that it’s very similar. So, we’ve done our transform correctly. And we’ll do now channel 3 for the flow rate. In order to do this, we need to know the flow rate, maximum flow rate for a mass flow control valve. So, we’ll check the flow rate on the label. It’s 200 milliliters a minute. So, we’ll enter a linear transform with a multiplier of 40, because 40 times 5 is 200. Again, check the values in the monitor window. Notice the flow rate now says 200. And our mass flow valve also says 200. For the fourth channel, the baseline data, we will leave it untransformed, because this parameter takes on fixed values of 0.5 or 0.2 as it switches between chamber and baseline. These can later be converted to ones and zeros in a macro.

This concludes setting up the data acquisition channels. And at this point, it’s advisable to save our data acquisition setup. So, click on Setup to save this part of the setup file configuration. Choose Save Setup. For convenience, we’ll save this file to the desktop. And we’re going to call it SmallAnimal1. Then you click the Save button.

Setting up the digital controls to regulate between chamber and baseline is a bit more demanding. Here we will generate a baselining profile to load. In the Acquisition Parameters tab, click on Digital Control, then click on During Recording. Make sure that the Enable During Recording Output box is ticked and active. And then click on the Synopsis to inspect the layout of an event’s profile. The columns Sample, Output Code, Marker, and Pause are the keys for generating your own digital control profile.

While a custom profile can be specified one event at a time in an editing window, the process is complex, and errors require that you start over from the beginning. It’s advisable to use a spreadsheet for a more versatile editing process. However, before starting a digital profile, we must first establish the recording duration. In this case, we’ll select a 16-minute recording, which is 960 samples at 1 Hz.

Now we can prepare the During Recording digital control output events. For these digital events, we’ll start with a baseline before switching to the chamber, and repeat these two more times, then end on a baseline. So, baseline, chamber, baseline, chamber, baseline, chamber, baseline. We’re going to make each of our baseline readings, or baseline dwell times, 60 seconds long. And we’re going to read from each chamber for 240 seconds. Cumulatively, this is 960 seconds, or 16 minutes. We’ll also use B as a baseline marker and C as a chamber marker to bracket the baseline and chamber events with distinct marker pairs. And finally, we’ll add a 60-second pause at the start of each chamber dwell time. Since the chamber has no airflow during baseline measures, it’s advisable to flush the chamber of accumulated CO2 before continuing respiratory measures.

So, we’re going to open an Excel spreadsheet. And we’re going to title the digital control columns with the digital control profile column names. Sample number, code, marker, and pause. And now we’ll enter the first sample, 0. The code is 1 because we’re on baseline. The marker will be B for baseline. And we will have no pause because a pause is not necessary at the start of the baseline. Our baseline is going to end 60 seconds later at sample 59. And again, we will enter a code, 1, marker B, and pause 0. Now we’re going to increment just one sample to sample 60 to start our first chamber sampling period. So, enter 60. And our code will be 0 for the chamber, a marker C, and a pause of 60. We’re going to allow one minute of flush before we start recording from the chamber.

Now we’ll move forward 240 samples to 299 for a 4-minute chamber sampling period. So, we’ll enter a 299, 0, C, and 0. No pause is necessary at the end of a chamber sampling period. Again, we will move forward just one sample to 300 and start a baseline,1B0, 359 to end the baseline, 1B0, 360 to start the next chamber dwell time – 0, C, 60, 599, 0, C, 0. This is time consuming, so we’ll fast forward to the last baseline. Note we have pauses only at the start of each chamber sampling period. We don’t need them at the end or at the start of the baselines.

Now we’re going to save this profile for future use. We’ll save it in comma-delimited format, a CSV file. And now we can select just the digital events and not the column titles. Copy that section of data. And we’re going to go back to Expedata, open our digital control, and select During Recording again. And click on Paste Events to transfer the copied events to Expedata. Then click on the synopsis and compare that synopsis with the events in our Excel file. Satisfy yourself that the events, that the numbers in the rows and columns are identical. Then you can click on exit.

And we’re going to save our setup file one more time. We’ll save it again as SmallAnimal1. Yes, we want to replace it. Our setup file is saved. And the small animal respirometry system now has a working setup file and you can go on to collecting data.