MouseOx Life Science Data Acquisition & Analysis

The MouseOx system was developed by a team of research engineers to simplify both data acquisition and analysis in life science applications. Data collected during an experiment is stored in a TDMS format file, which contains all recorded parameters. These files can be opened in the MouseOx Playback Software, where results are displayed graphically.

Within the playback environment, researchers can view, zoom, and compress data, as well as select specific sections to export into Excel for further analysis. Each parameter in the dataset is accompanied by error codes, ensuring data quality and traceability. Importantly, all data is captured on a beat-by-beat basis rather than averaged — a design intended to provide rapid feedback during surgical monitoring. For deeper analysis, however, users may choose to apply averaging across defined sections of the file to generate broader statistical insights.

To support different research applications, we’ve produced three detailed Standard Operating Procedures (SOPs):

• Single Animal Monitoring
• Multiple Animals with Multiplexer
• Multiple Animals with Simultaneous Software

Each SOP provides step-by-step instructions for setup, data collection, and downstream analysis using Excel templates.

Single Animal Data Collection and Data Analysis SOP

This document is intended to show all the steps and options for monitoring an awake/single mouse. This document will also show the steps for analyzing the collected data by using an Excel template.

Step 1: Set-Up System & Connect Animal

Connect the awake animal to the MouseOx system. If the mouse’s hair is a color other than white, shave small patches of hair on the neck where the LED and photodetector make contact. Hair on the back of the neck will help the sensor fit more securely. The enclosure for the animal should also be set up to minimize reflected light, with bedding, paper towels, or a surgical pad placed inside.

Configure the system for awake animals:

Mode: This setting tells the software how to control the signal. Awake Mode enables motion detection and rejection and keeps the signal smaller so that motion artifacts are amplified less

Animal Type: This setting informs the software of the species being monitored so it can optimize the signal appropriately and determine the level of control required at startup

Sensor Type: This setting ensures the software uses the correct saturation calibration curve, which is especially important for ranges below 80%.

Step 2: Monitor Animal & Start Saving Sata to the TDMS File

Select the green “Play” button so the system starts acquiring a signal. Move the motion sensitivity slider to the least sensitive setting to increase the likelihood of valid calculations. Once valid calculations appear, select the “Start Recording” button to begin saving data to the TDMS file. After collecting the desired data, select the “Stop Recording” button to end the saving process, then press the red “Stop” button to halt data acquisition. Finally, press the “Main Menu” button to proceed to the collected data.

Step 3: View Data in Playback

Select the “Open file” button to access a previously saved TDMS file. Optionally, use the “Visible Channels” feature to hide channels that are not needed for the experiment.

Step 4: Select Data for Export to Excel

Click and hold the left mouse button on the cursor at the left side of any graph and move it to the desired start point of the data you wish to export. Select the “Set” button under Start Time. Then move the cursor to the end point of the desired data range and select the “Set” button under End Time. Leave all other export options at their default settings.

If the data to be exported is very large, consider exporting at a slower sample rate. The default is 15 Hz, but options are available to create the export file at 5 Hz or 1 Hz.

Step 5: Use a Template to Analyze Data

To use the Excel template to analyze the exported data, open both the export file and the template file in Excel.

Use the Excel template to analyze the exported data. Open both the export file and the template file in Excel. Copy columns A–N from the export file and paste them into the template. Save the template file under a new name, then scroll to the right side of the screen to view the statistical summary of the collected data.

In this example, 2,558 points were collected. At 15 Hz, this equates to 2.84 minutes of data (2,558 points ÷ 15 Hz ÷ 60 seconds). Of those, 151 valid saturation points were collected, representing approximately 10 seconds of valid saturation data (151 points ÷ 15 Hz).

Multiple Animals with Multiplexer Data Collection and Data Analysis SOP

This document outlines all the steps and options for monitoring multiple awake mice using the MouseOx system with the Multiplexer. It also describes how to analyze the collected data using an Excel template.

Step 1: Set-Up System & Connect Animals

If the animals’ hair is a color other than white, shave small patches of hair on the neck where the LED and photodetector make contact. Hair on the back of the neck will help the sensor fit more securely. The enclosures for the animals should also be arranged to minimize reflected light, with bedding, paper towels, or a surgical pad placed inside.

Configure the system for awake animals:

Mode: This setting informs the software how to control the signal. Awake Mode enables motion detection and rejection and keeps the signal smaller, reducing the amplification of movement artifacts.

Animal Type: This setting tells the software the species being monitored so it can optimize the signal appropriately and determine the necessary level of control at startup.=

Sensor Type: This setting ensures the software uses the correct saturation calibration curve, which is especially important for ranges below 80%.

Step 2: Monitor Animals & Start Saving Data to the TDMS File

Select the green “Play” button so the system can start acquiring a signal. Move the motion sensitivity slider to the least sensitive setting to maximize valid calculations. Once valid calculations are present, select the “Start Recording” button to begin saving the TDMS file.

Set up the ”Auto-Cycle” features in the Multiplexer controls Menu screen:

Turn on the required multiplexer channels and enter animal identifiers if relevant, then select the “Auto-Cycle” button. In the “Auto-Cycle” options portion of the window, choose the target parameter and time interval. This ensures the system collects valid data for the specified parameter before switching to the next subject. For example, you might set the system to record 5 seconds of valid saturation before switching animals.

The above example shows 5 seconds of valid Saturation before switching. Enable the “Time-Out Limit” and select a valid time out time. This will force the system to switch animals even if the desired time interval isn’t achieved, preventing the system from getting stuck on one subject

After collecting the desired data, select the “Stop Recording” button to end the file saving process, then press the red “Stop” button to halt data acquisition. Finally, select the “Main Menu” button to access the collected data

Step 3: View data in Playback

Select the “Open file” button to open a previously saved TDMS file. Optionally, use the “Visible Channels” feature to hide any channels not needed for the experiment.

Use the Compression options to zoom in on the saved data points. When working with multiple animals, the cursor data will represent all calculated parameters for the selected subject (for example, subject 2 if the cursor is on subject 2, or subject 1 if the cursor is on subject 1). Data points between subjects will be flagged with error codes to account for the transition period as the system adjusts between animals. These delays occur because filtering is applied to the signals during switching.

Step 4: Select Data for Export to Excel

In this example, the steps are visible in the file marker channel, so select a segment of data before the file marker changes to capture baseline parameters for both subjects.

Click and hold the left mouse button to grab the cursor at the left side of a graph and move it to the desired start point. Select the “Set” button under Start Time. Move the cursor to the desired end point and select the “Set” button under End Time. Leave all other export options at their default settings.

If the data set is very large, consider exporting at a slower sample rate. The default is 15 Hz, but options for 5 Hz or 1 Hz are available.

Step 5: Use a Template to Analyze Data

Open both the export file and the template in Excel.

Copy columns A–N from the export file into the template. Save the template under a new name, then move to the right portion of the screen to view the statistical summary of the collected data.

Summary data:

In this example, the experiment measured baseline parameters before an event. The average data for each animal is summarized as follows:

• Subject 1: 5,173 sample points collected, equivalent to 17.24 minutes of data (5,173 points ÷ 5 Hz ÷ 60 seconds).
• Of this data, 1,249 valid saturation calculations were recorded, representing 4.16 minutes of valid saturation data (1,249 points ÷ 5 Hz ÷ 60 seconds).

Graphable data:

The data can also be filtered by subject number and error code. For graphing, valid data for each subject can be isolated under the corresponding column headers. For example, subject 2’s valid data can be found under its designated yellow column.

Multiple Animals with Simultaneous Software Data Collection & Analysis

This SOP outlines all the steps and options for monitoring multiple awake mice using the MouseOx system with the Multiplexer. It also describes how to analyze the collected data using an Excel template.

Step 1: Set-Up System & Connect Animals

Set up the MouseOx 3.0 software to run multiple MouseOx systems on one computer. See the “MouseOx 3.0 / 2.0 Quick Start Guide” for more detail. In short, the MouseOx® Plus system with the Simultaneous product key must be connected and detected by the MouseOx 3.0 software. Once this Simultaneous product key is accepted by the MouseOx 3.0 software, then anytime this MouseOx is detected by the software, all other MouseOx systems will be accessible.

Each MouseOx system must be configured and confirmed. This allows for each system to get the relative constants applied to each of the products. If different sensors are being used or different animal types, this configure and confirm step will address it.

Custom ID/Name: If a Custom ID is required then this must be keyed in here before the system is started.

Blink Sensor: This button can be pressed to determine which MouseOx these settings are being applied to. At this release of the software the MouseOx systems are put into the order by how the user’s computer detects them and how InstaCal organizes them.

Mode: This lets the software know how to control the signal. Awake Mode allows for motion detection and rejection. Awake Mode also keeps the signal smaller so that motion is amplified less.

Animal Type: This lets the software know how to best optimize the signal. This indicates to the software what level of control is required at start up.

Sensor Type: This lets the software know which saturation calibration curve to use. This is very important for saturation ranges below 80%.

Confirm: This button must be clicked for each MouseOx detected before the software will allow the “START” button to be selectable. This button click locks in the constants for each animal.

If awake animals are being used:

Connect the awake animals to the MouseOx system. If the mouse hair is a color other than white shave little patches of hair on the animals’ neck where the LED and photo detector of the sensor touch the animal. Hair on the back of the neck will help the sensor fit better.

The enclosures for the animal should be set up in such a way that reflected light is minimized. Bedding, paper towel or a surgical pad should be placed in the enclosure.

Step 2: Monitor Animals & Start Saving Data to the TDMS File

Select the green “Play” button to start acquiring a signal from the animal. Move the motion sensitivity slider to the least sensitive setting to maximize valid calculations. Use the MouseOx Navigation menu to access the other systems and start them as well.

The green “Play” button on the MouseOx #1 form acts as the master start button. If pressed, it enables the “Play” buttons on the other systems to be activated. If the other systems have already been started, pressing the master “Play” button will begin recording across all devices simultaneously.

The “Tile Display” button on MouseOx#2-#6 venly distributes the monitoring windows across the desktop for easier viewing. Once valid calculations are detected, select the “Start Recording” button on the MouseOx#1 form to begin the file saving process.

After desired valid data is collected select the “Stop Recording” button to end the file saving process. Press the red “Stop” button to stop data acquisition. Press the “Main Menu” button so we can go look at the collected data.

Step 3: View data in Playback

Select the “Open file” button to open a previously saved TDMS file. Optionally, use the “Visible Channels” feature to hide channels that are not relevant to the experiment.

Use the Compression options to zoom in on the data to see the saved data points in more detail if desired. This data illustrated represents 6 awake animals. The cursor data represents all calculated parameters for all subjects, with results color-coded by layer. Each animal’s data layer can be individually displayed or hidden by selecting the checkboxes in the upper right corner of the screen.

Step 4: Select Data for Export to Excel

In this example, steps are visible in the file marker channel, so select a segment of data before the file marker changes to capture baseline parameters for the six subjects.

Click and hold the left mouse button to move the cursor to the desired start point. Select the “Set” button under Start Time. Then move the cursor to the desired end point and select the “Set” button under End Time. Leave all other export settings at their defaults.

If the data set is very large, consider exporting at a slower sample rate. The default is 15 Hz, but files may also be exported at 5 Hz or 1 Hz to reduce size.

When the “Create File” button is selected, the software will generate six Excel files — one for each animal.

Step 5: Use a Template to Analyze Data

Open both the exported file and the template file in Excel. 

Copy columns A–N from the export file and paste them into the template. Save the template under a new name, then move to the right portion of the screen to view the statistical summary of the collected data.

In this example, 2,558 points were collected, which equals 2.84 minutes of data at 15 Hz (2,558 points ÷ 15 Hz ÷ 60 seconds). Of these, 151 valid saturation points were recorded, representing 10 seconds of valid saturation data (151 ÷ 15 Hz).

Repeat this process for each animal to get summary data for each animal.

Date Analysis Templates

After collecting data with the MouseOx system across different applications, the next step is to make sense of that information. To support researchers, we’ve developed several Excel templates that serve as starting points for data analysis. These templates provide a framework for filtering, organizing, and summarizing experimental results, with the flexibility to be adapted as studies become more complex.

There are 4 templates so far that are available. As we learn more about our customer needs, more templates will be made.

• Awake/single animal Template
• Multiple animal Template
• File marker Template
• Computer clock Template

Awake/Single Animal Template

This template just filters the collected data based on the error code channel alone. The following table list the error codes:

Data gets pasted in columns A-N:

Filtering is done in columns O-Y:

The statical summary is in columns AB-AF:

This is the basic format of how the templates all work, so the details will be less for the more complex filters that follow.

• The data always gets pasted in columns A-N
• the filtering will start at column O and using as many columns as needed.
• The statistical summary results will always be in the column next to the filtering columns.

Multiple Animal Template

This template filters the data based not only on the error code channel but also on the subject number channel. This allows each animal to have its own independent statistical summary. The results of this filter provide a clear breakdown of valid data by subject, enabling direct comparison between animals in multi-subject studies.

The results of this filter look like this:

File Marker Template

This template filters the data based on the error code channel and the file marker channel. File markers can be inserted during recording by pressing the file marker button, or a file marker channel can be created in Excel afterward based on the experimental design and requirements. 

The results for this filter look like this:

Computer clock Template

The newest template filters data using both the error code channel and the computer clock channel. Currently, it is configured to start at the beginning of the dataset and perform statistical analysis in five-minute intervals. This approach makes it especially useful for long-duration studies where changes need to be tracked consistently over time. The results are displayed as a series of time-based summaries, providing a high-level overview of experimental trends.

The results for this filter look like this:

Turning MouseOx Life Science Data Acquisition into Actionable Insights

MouseOx is more than a pulse oximeter — it is a complete workflow for life science data acquisition and analysis. From SOPs that ensure reliable signal collection, to TDMS file management and Excel templates that transform raw values into statistical summaries, MouseOx provides researchers with every step needed to move from experiment to insight.

By implementing MouseOx in your laboratory, you can:

• Confidently acquire valid, beat-by-beat data in both single and multiple animal studies.
• Streamline data filtering and analysis with structured templates.
• Generate reproducible results that strengthen scientific conclusions.

The result is faster, more accurate research with tools that adapt as your studies grow in complexity. MouseOx empowers scientists not only to collect data but to transform it into discoveries that drive life science forward.