Faq's

When starting AutoResp™ and this error message appear, AutoResp™ was not installed with administrator rights. During the AutoResp™ installation process, a file must be copied into a Windows system folder. This requires an administrator login. Here is the instruction how to install the necessary file to get rid of the error message:

1. Login as an administrator
2. Download the following configuration file (LINK) and save the file to your desktop.
3. Locate the folder folder: C:\ProgramData\Measurement Computing\DAQ\ . The folder Program Data is a system hidden folder. So you might have to change settings for the folder in order see hidden folders and system files. Hidden folders are shown as “transparent” in Windows’ file explorer.
4. If the folder doesnt exist, please create it.
5. Now move the file into this folder.
6. After you moved the file, change folder settings again to hide hidden and system files.
7. Start AutoResp™. The error message should be gone by now.

If the display on your OXY-REG is giving the error message "SE.BR" (sensor breakage), it means that the signal input type for the instrument has been changed from the default setting (potmeter).

To change the input type back to the default setting, press the OK button once. Then press the arrow buttons until the input type POTM (potmeter) is shown in the display and then press OK to choose this. Finally exit the set up menu by pressing the OK button several times until the display shows - - - -.

Tracking requires two synchronized (in time) cameras to track animals in three dimensions.

Mount the two cameras with a 90° angle in between, e.g. one camera filming from above and one filming from the side.

Simultaneous video recordings from both cameras can then be analyzed in LoliTrack to get two pairs of X-Y coordinates.

In this way, one pair of X-Y coordinates translates into the third (Z) coordinate. See the figure below.

This guide shows you how to draw zones and mask in LoliTrack and ShuttleSoft.

Use the Circle button, then draw a circle in one of the compartments. Afterwards, click on the Mask Inside Area button. 

Use the Circle button again to draw a circle in the other compartment. Afterwards, click on the Mask Inside Area button.

Use the Rectangular button, then draw a rectangle between the two compartments. Afterwards, click on the Mask Inside Area button.  

Now invert the mask by clicking on the Invert Mask button. 

Draw a rectangular area in one compartment, and click on a Zone button (A, B, C...). This area is now defined as a zone of interest. 

Draw a rectangular area in the other compartment, and click on a different Zone button. This area is now also defined as a zone of interest. 

This is an example of how a typical mask and zones could look like running a ShuttleSoft experiment.

To change the language in the PIT tag reader software (APR-PC-DEMO) from German to English, please go to the following program files folder on your PC:

1. Locate C:\Program Files (x86)\AgriDent
2. Delete the file(s) that has the *.lng file extension (e.g. Agrident.lng).
3. Without this language file, the software will now use the default language (English).

Loligo^® Systems offers the three main types of oxygen sensors differing in measuring principle, response time, sensor size, maintenance requirement and pricing.

1. Optical oxygen sensors
For many invasive techniques, measurements in tiny volumes (e.g. micro respirometry) or applications which require high temporal and spatial resolution, fibre-optic oxygen sensors are the only solution.

Even for general purposes we recommend optical oxygen sensors featuring low maintenance requirements, high stability and accuracy, no electrical interference, no ground loop problems, and zero O₂ consumption by the sensor.

The main disadvantages is price, single-channel meters start at about €3750. A high temperature sensitivity of this technology and a fragile tip on the <50-140 nm micro sensors might also be a problem in some applications. The macro sensors, on the other hand, are very tough.

2. Galvanic cell oxygen electrodes
Galvanic type oxygen probes are inexpensive and rugged sensors producing a milliVolt signal for easy instrumentation without supplying power. 

We recommend galvanic probes for applications like respirometry and field measurements, and as a low-budget alternative to optical oxygen equipment, e.g. for multi-channel systems. They can be used with relatively long cables (+25 meters). We recommend using a galvanic isolation preamplifier between the probe and any data acquisition system to minimize possible ground loop problems.

The main disadvantage of galvanic probes is a relative long response time and oxygen self-consumption making them unsuitable for measurements in small volumes and in un-mixed samples.

3. Polarographic oxygen electrodes (or Clark type electrodes)

Low oxygen self-consumption and a small size make these sensors suitable for physiological setups like blood gas analysis and low volume respirometry.

However, Clark type electrodes require much maintenance, often membranes and electrolyte fluid should be changed on a daily basis, and polarographic amplifiers for these sensors are quite costly.

Thus, we recommend the E101 as a replacement oxygen electrode for customers with their own polarograhic oxygen meter, e.g. PHM meter from Radiometer Copenhagen, OM200 from Cameron Instr. Co. etc.

CALIBRATION PRINCIPLE
Instrument calibration is an essential first step in analytical and measurement procedures. The rationale for a two-point calibration is to provide two points of reference with which to calibrate the instrument and, therefore, ensuring accurate measurements with your sensor of the unknown concentrations of your samples.  A two-point calibration between two extremes are advocated, e.g. 0 - 100 % air saturation.  For the low calibration point, we recommend using either nitrogen gas or sodium sulphite solution, for the high calibration point, bubble atmospheric air using an aerator.  Please see below for general step-wise instructions on how to carry out a two point calibration.  For specific instructions for a particular oxygen instrument, please click on the specific links.

GENERAL

1. Connect the probe to the oxygen instrument and turn on the instrument.
2. Place the tip of the probe in a mixed air-equilibrated water sample. This can be achived by purging atmospheric air into sample water, e.g. with an air pump and air stone.
3. Wait for the reading to stabilize. Then save this point as the HIGH calibration value (100% air saturation).
4. Place the tip of the probe in an oxygen free water sample (e.g. by purging nitrogen gas into sample water or by dissolving ~10 grams of Na₂SO₃ in 500 mL of distilled water).
5. Wait for the reading to stabilize. Then save this point as the LOW calibration value (0% air saturation).
6. Rinse the probe with distilled water.
7. Place the probe into the sample, and record the sample oxygen saturation when the reading is stable.

See below for a diagrammatic representation of sensor readings at:

1. 100 %  to 0 % air saturation
2. 0 % to 100 % air saturation
3. 100 % to 0 % and back up to 100 % air saturation.

100% to 0% air saturation	0% to 100% air saturation
100% to 0% to 100 % air saturation

The oxygen sensor spot should be integrated into a dry, clean vessel (humidity or oily residues affect the adhesion and may lead to a detaching of the sensor spot from the vessel wall). The adhesion surface area of the vessel wall should be plane or slightly arched but not strongly curved or corrugated. Otherwise, the spot may detach partly from the vessel wall during the curing process of the silicon glue due to the tension of the spot.

The silicon glue should be cured for at least 60 min. before the test vessel is fill.

Apply a small amount of silicon glue (D5-Spot: ca. 4 µL) onto the red side of the spot.


Position the spot on the plane bent end of a spatula.


Attach the spot to the inside wall of the test vessel.


Shift the sensor spot slightly with little pressure onto the surface so that a small ring of silicon glue emerges around its edge.


No air should be enclosed in the silicon layer between spot and vessel wall.


Silicon stains on the black sensor surface should be avoided since they increase the response time of the sensor.

The light from the blue-green LED excites the oxygen sensor to emit fluorescence. If the sensor spot encounters an oxygen molecule, the excess energy is transferred to the oxygen molecule in a non-radiative transfer, decreasing or quenching the fluorescence signal. The degree of quenching correlates to the partial pressure of oxygen in the matrix, which is in dynamic equilibrium with oxygen in the sample. The decay time measurement is internally referenced.

The Loligo^® shuttle tanks are modified versions of the classic operant conditioning chambers (also known as the Skinner box) used for experimental analysis of behavior, e.g. to study operant conditioning and classical conditioning in animals.

An operant conditioning chamber permits experimenters to study behavior conditioning (training) by teaching a subject animal to perform certain actions (like pressing a lever) in response to specific stimuli like a light or sound signal. When the subject correctly performs the behavior, a mechanism delivers food or another reward. In some cases, the mechanism delivers a punishment for incorrect or missing responses.

With this apparatus, experimenters perform studies in conditioning and training through reward/punishment mechanisms. Operant chambers have at least one operandum, that can automatically detect the occurrence of a behavioral response or action.

Typical operanda for primates and rats are response levers. Despite such a simple configuration (e.g. one operandum and one feeder), it is possible to investigate many psychological phenomena in this way.

For this reason, operant conditioning chambers have become common in a variety of research disciplines including behavioral pharmacology, and Skinner's Box have been used extensively for behavioral research in primates and rats.

Loligo^® shuttle tanks have been developed for aquatic animals, like zebrafish or crustaceans, and the tank design allows for independent control of water quality in two sub compartments. Tank dimensions are made special to accomodate a wide variaty of animal species and sizes.

Inside the Shuttle tank, the animal can freely "shuttle" between two sub compartments with opposite acting controls.

The computerized Loligo^® shuttle systems are equiped with a video camera and lighting conditions enabling real-time pc vision software to detect animal locomotion.

If the animal changes its position from one user-defined zone to the next through locomotion, the computer software (ShuttleSoft) activates/deactivates programmed devices to change environmental conditions inside the tank, e.g. to regulate water temperature to preferred values through behavior. Or you can set up two different (constant) temperature levels in the two tank compartments independent of fish behavior for exposure/avoidance/choice tests.

Today, a main application of Loligo^® shuttle tanks measurements of temperature preference in aquatic ectotherms (as well as avoidance behavior), and automated computerized systems, have been made for a range of other environmental factors like water turbidity, salinity, oxygen saturation, pH and pCO2.

The turnkey systems offered include everything needed for video behavior analysis as well as monitoring and regulating water quality.

Intermittent flow (or stop-flow) respirometry - Principles and Background

Measurements of oxygen consumption rates on fish and other water breathers commonly involves using one of three different methods:
 
1. Closed respirometry (or constant volume respirometry) 
2. Flow-through respirometry (or open respirometry) 
3. Intermittent flow respirometry (or stop-flow)

1. Closed respirometry (or constant volume respirometry)

Measurements in a sealed chamber of known volume (a closed respirometer). The oxygen content of the water is measured initially (t0), then the respirometer is closed and at the end of the experiment (t1) the oxygen content is measured again. 
Knowing the body weight of the animal, the respirometer volume and the oxygen content of the water at time t0 and t1, the mass specific oxygen consumption rate (mg O₂/kg/hour) can be calculated as follows:

• [O₂]_t0 = oxygen concentration at time t0 (mg O₂/liter)
• [O₂]_t1 = oxygen concentration at time t1 (mg O₂/liter)
• V = respirometer volume minus volume of experimental animal (liter)
• t = t1 – t0 (hour)
• BW = body weight of experimental animal (kg)

An advantage of this method is its simplicity. A disadvantage is that the measurements are never made at a constant oxygen level, due to the continuous use of oxygen by the animal inside the respirometer. This might cause problems when interpreting data, since animal respiration often changes with ambient oxygen partial pressure.
Furthermore, metabolites from the experimental animal, i.e. CO₂, accumulate in the water, thus limiting the duration of measurements. This limited time for measurements prevents the experimental animal to recover from initial handling stress that often increase fish respiration significantly and for several hours, thus overestimating oxygen consumption rates.

2. Flow-through respirometry (or open respirometry)
This is a more sophisticated method for oxygen consumption measurements. Experimental animals are placed in a flow-through chamber with known flow rate. Oxygen is measured in the inflow and outflow and oxygen consumption rate (mg O₂/kg/hour) can be calculated as:

• F = water flow rate (l/hour)
• [O₂]_in = oxygen content in water inflow (mg O₂/liter)
• [O₂]_out = oxygen content in water outflow (mg O₂/liter)
• BW = body weight of experimental animal (kg)

The advantages of this method are several:

1. The duration of the experiment is in principle unlimited
2. No accumulation of CO₂ and other metabolites
3. Its possible to measure at a constant oxygen level
4. By controlling the quality of the inflowing water its possible to measure metabolism at different desired levels of oxygen, salinity etc.

However, this method bring along one significant disadvantage: In order to determine oxygen consumption by open respirometry it is crucial that the system is in steady state. This means that the oxygen content of the in-flowing and out-flowing water, AND the oxygen consumption of the animal, have to be constant. 
If the oxygen consumption of the animal for some reason changes during the experiment, steady state will not exist for a while. The above formula will not give the correct oxygen consumption rate until the system is in steady state again. The duration of the time lag depends on the relationship between chamber volume and flow rate. Thus, open respirometry measurements have poor time resolution and are not suitable for determination of oxygen consumption on organisms with a highly variable respiration like fish.

3. Intermittent flow respirometry
Our system for automatic respirometry works by intermittent flow respirometry aiming at combining the best of both 1) closed and 2) flow-through respirometry.

• The experimental animal is placed in a respirometer immersed in an ambient tank (temperature bath).
• A recirculating pump ensures proper mixing of the water inside the respirometer and adequate flow past the oxygen probe. 
• A second pump can swap the water inside the respirometer with water from the ambient tank (temperature bath). During measurements of oxygen consumption, this flush pump is turned off and the systems operates like a closed respirometry setup. 
• Then the pc controlled flush pump turns on pumping ambient water into the respirometer and bringing the oxygen content back to pre measurement levels.
  In this way, problems with accumulating metabolites and severe changes in oxygen level due to animal respiration are avoided.
• As with open respirometry, the duration of the experiment is in principle unlimited.

However, the most important advantage is the great time resolution of this method. Oxygen consumption rates of animals can be determined for every 10th minutes over periods of hours or days, making our systems for automatic respirometry extremely suited for uncovering short term variations (minutes) in respiration.

In summary, our system for automatic respirometry is developed for prolonged and automatic measurements of oxygen consumption rate in a controlled laboratory environment.

The automatic measuring proceedure runs in 3 phases:

1. Measuring period
2. Flush period
3. Wait period

In the Measuring period (1) the flush pump is off, and the chamber is closed. Fish respiration rate is calculated from the decline in oxygen. During this time the recirculation pump is active to mix the water inside the respirometer and to ensure proper flow past the oxygen sensor.
The measuring period is followed by a Flush period (2) where the flush pump is active pumping water from the ambient temperature bath and into the respirometer. During this period the recirculation pump is inactive and the oxygen curve will raise to approach the level of the amient water.
Finally, the flush pump stops and the loop ends with a short Wait period (3) before starting a new measuring period. This waiting period is necessary to account for a lag in the system response resulting in a non-linear oxygen curve. During the Wait period the recirculation pump is active.

Examples of raw MO₂ data

Standard metabolic rate of juvenile Rainbow Trout was determined in static respirometer chambers and with an automated respirometry system from Loligo^® Systems. Initial high oxygen consumption rates due to handling stress, were followed by a gradual decline to lower and more stable values indicating standard metabolic rate for the specimen. Notice the high temporal resolution (10 min) of the system revealing sudden changes in MO₂.

Courtesy by J.Svendsen/DIFRES & J.Lund/Univ. Aarhus

The chamber should be large enough to house the intact animal, but not much larger as it will leave space for unwanted activity like swimming that will make it harder (and take longer) to determine resting/standard/minimum metabolic rate.

The chamber volume should be kept at a minimum for reliable respiration measurements to get a better temporal resolution and signal-to-noise ratio. If the volume is too large, the resulting oxygen depletion curve will be too flat for solid estimates of the slope that is used in the calculation of the oxygen consumption rate (MO₂).

As a rule of thumb, we recommend a resting chamber with a volume up to 50 times the volume (≈ wet weight) of the animal:

Use a 500 mL chamber for fish weighing down to 10 g (ratio = 500/10 = 50).

A lower ratio might be needed as the mass specific respiration rate of ectotherm animals, like fish, scales with body size (i.e., large animals have lower mass specific O₂ consumption rates than smaller animals) and temperature (i.e., high temperature = high respiration and vice versa), and also differs between species (e.g., a sluggish benthic fish species often have a lower mass specific metabolic rate than an active pelagic species).

Thus, use a smaller chamber (ratio) if working with large and sluggish arctic fish, e.g., a 15 L chamber for fish weighing down to 1 kg fish (ratio = 15/1 = 15).

Active fish swimming in a tunnel respirometer have high mass-specific oxygen consumption rates (MO₂), allowing reliable oxygen consumption estimates in relative higher respirometer volume than for static respirometry. Tunnel respirometers are difficult to build with a fish volume to respirometer volume of less than 1:100. We recommend a maximum ratio between the wet weigth (or volume) of the fish and the volume of the swim respirometer of 1:200, e.g. a 90 liter swim respirometer fits fish down to app. ½ kg. If the volume is too large, the resulting oxygen curve will be too flat for reliable estimates of the slope that is used in the calculation of oxygen consumption rate (MO₂).

Another restraint is the dimensions of the test section, which should allow the experimental fish to perform unrestricted swimming. This will largely depend on the species and mode of swimming.

Please contact us to get free advice on which swim tunnel that will be best for your project.

To wash out a tube-shaped respirometer chamber requires a volume ~5 times that of the chamber.

Thus, if you use a pump delivering a flow per minute equal to the chamber volume, then a 5 minutes flush period will ensure that 99 % of the water is replaced during each flushing cycle.

Stronger pumps might create too strong a flow forcing fish to struggle or unwanted activity. Lower flows require longer time for flushing, and this will decrease time resolution of MO₂ data.

Some materials, like Plexiglass/Perspex can act as oxygen stores and sinks, forming pools of oxygen which can be released or stored in a reversible way - see Stevens, J. (1992) J. Appl. Physiol. 72, 801-804. 

This can have an important effect when chambers are down-scaled for micro respirometric measurements of very low oxygen fluxes. 

Thus, for oxygen measurements in small volumes less than a few millilitres (mL), we recommend chambers of glas and inert components with non or low oxygen storage capacity! 

For respirometers with larger volumes (>½ litre), the use of acrylic materials have no significant effects on measurements.

If you purchased a software upgrade, please follow the steps below to add new license codes to your WIBU dongle:

1. Download the following info file (LINK) and save the file to your desktop.
2. Double-click it to transfer license codes from your dongle (connected to your PC) and save it to a .wbc file.
3. Email the .wbc file to this address: mail@loligosystems.com.
4. We will then quickly return a .rtu file as an email attachment. This .rtu file carries the new license code(s).
5. Save the .rtu file on your desktop.
6. Double-click the .rtu file to transfer new license code(s) to the dongle connected to your PC.
7. Finally, download the upgraded version of the software from our website and install it.

If the Input [phase], Oxygen [%air sat] and Temperature [^OC] shows NaN (Not a Number), you should check the following:

1. Select the right Witrox instrument for the Oxygen input channel (see image above)
2. Select the right Witrox instrument for the Temperature input channel (for real-time compensation).
3. Check that the fiber optic cable and the Pt1000 temperature probe (red mark on cable must match red mark on Temp input) is connected correctly to the Witrox instrument (see below):

The NaN should now be replaced by data values.

If the Input [phase] and Temperature [^OC] shows NaN (Not a Number), you should check the following:

1. Select the right Witrox instrument for the Temperature input channel (see image above).
2. Check that the Pt1000 temperature probe is connected correctly (red mark on cable must match red mark on Temp input) to the Witrox instrument:

The NaN should now be replaced by data values.

If the Board number for the DAQ-BT disappears after having selected it, there could be two reasons:

1. You have not selected the correct board number.
2. A board number has not been configured for the device.

Solutions:

1. Select the board number that has been configured for the instrument.
   1. Tip: Open the software InstaCal to check the correct board number (here Board# 0):
      
      
      
2. Configure a board number for the DAQ-BT device.
   1. Exit AutoResp.
   2. Open the software InstaCal as administrator (right-click).
   3. InstaCal will now configure the instrument automatically. Click OK to the following message:
      
      
   4. Click OK to the following message:
      
   5. Use the board number you see here (e.g. Board# 0):
      
   6. Click File > Exit
   7. If the following error message appears, you must exit InstaCal and open it again as administrator:
      

If the Calibration error appears, you need to calibrate (or re-calibrate) the oxygen sensor. Please refer to this FAQ for instructions on how to calibrate an oxygen sensor.

If the ERROR: Instrument 1 (or 2/3/4) appears, you should check:

1. If you have selected the assigned COM port for the Witrox instrument.
2. If the Witrox instrument is ON and within (Bluetooth) range of the computer.
3. If the Witrox instrument is paired with the computer.
   • Tip: Check your connected Bluetooth devices list (see Other devices).
4. If the Witrox instrument has timed-out (warning icon on the instrument will light red when timed-out).

Solution:

Close the error-window.

1. To find the assigned COM, please try:
   1. In Windows 10: Go to Control Panel > Devices and Printers > Find the paired Witrox device > Right-click on the device icon > Choose Properties > Choose the Hardware tab > Look for the COM port under Standard Serial Connection via Bluetooth (COM#) > Use this COM-port in AutoResp™.
2. Turn the Witrox instrument ON and secure a free line of sight to the computer avoiding metal or magnetic objects that can block wireless communication.
3. To pair the Witrox instrument to your computer, please try:
   1. In Windows 10: Go to Settings > Devices > Add Bluetooth or other device > Choose Bluetooth > Look for Witrox and choose “Pair”. If Windows asks for a pairing code, use “0” (zero).
4. Press the power button to turn the Witrox instrument OFF and exit the timed-out mode. Press the power button again to turn the Witrox instrument ON.

If the No COM port selected error message appears, you should check that you have selected the assigned COM port for the instrument indicated in the error window; here the first oxygen instrument, a Witrox 1.

If the No input for: Ambient oxygen N^o 1 error message appears, you should check:

1. If the oxygen sensor (fiber optic cable) is connected correctly to the Witrox instrument SMA connector:
   
2. If the fiber optic cable is damaged.
3. If the fiber optic cable is misaligned onto or at a distance from the sensor spot.
   

If the No input for: Ambient temperature N^o 1 error message appears, you should check that the Pt1000 temperature probe is connected correctly to the Witrox instrument (red mark on cable must match red mark on Temp input):

If the Input [RPM], Velocity [cm/s] or Output [V] shows NaN (Not a Number), you should check the following:

1. That the motor controller is powered ON and set to FWD/Forward.
2. That the OUT/IN on the back of the DAQ-BT is connected with the analog data cables to the IN/OUT on the motor controller:
   
3. That the knob on the motor controller is turned towards EXT:
   
   
4. That you have selected the DAQ-BT for the Velocity input channel and the correct Motor (type of swim tunnel):
   

You should now see data (RPM) values instead of NaN:

If the No device selected error message appears in AutoResp 2.3.0, you should delete the AutoResp configuration file:

1. Close AutoResp and all applications on your PC.
2. In Windows, go to: My computer > Programs (x86) > AutoResp > Delete the CONF-file named AutoResp.
3. Open AutoResp as administrator (you should always open as administrator).
4. The configuration file has now been reset and the error message should no longer appear.

The LoligoBT is a 4-fold power strip that is powered from a wall outlet and communicates with a Windows computer via Bluetooth 4.0. LoligoBT is used for wireless software control of equipment connected to one of the four independent electrical sockets, i.e., relays turning pumps, valves, stirrers etc. ON or OFF from a distance.

Important

• The LoligoBT is equipped with an ethernet port. The port is covered by a lid. You should NOT remove this lid or connect an ethernet cable to the LoligoBT. It will reset the device and void the warranty!

Setup:

1. Insert the small black USB dongle directly into your PC. Let the dongle configure itself in Windows.
   
2. Connect the LoligoBT into a wall socket.
3. Set the power switch to “l” to turn the LoligoBT on (see below):
   
   
4. Wait until the device is ready (see below). It takes about 50 seconds:
   
   
5. COM port number: In Windows 10, go to Settings > Devices > Look for the BLUEGIGA BLUETOOTH LOW ENERGY (COM#) > Make a note of this COM port number.
   • If Windows asks for a pairing code, use “123456”.
6. Open AutoResp™ as administrator (right-click).
7. Select the right COM port number for this LoligoBT device.
8. Your LoligoBT device is now ready to be used in AutoResp™.

The Witrox instruments are used for measuring dissolved oxygen using fiber optic mini sensors (optodes) and for measuring temperature.

Important

• Do not use the free WitroxView software while running AutoResp™ on the same PC!

Setup

1. To power the Witrox instrument, connect the DC adapter to a wall outlet and the USB power cable to the threaded socket on the backside of the instrument.
   • Tip: You can power a Witrox instrument directly from your PC using a USB cable.
2. Press the power button. The power LED will turn green. The link LED (wireless icon) will flash blue indicating that pairing mode is enabled.
3. Pairing in Windows 10: Go to Settings > Devices > Add Bluetooth or other device > Choose Bluetooth > Look for Witrox and choose “Pair”.
   • If Windows asks for a pairing code, use “0” (zero).
4. Verify that the Witrox is paired with your PC (under Devices in Other devices list).
   
5. COM port number: In Windows 10, go to Control Panel > Devices and Printers > Find the paired Witrox device > Right-click on the device icon > Choose Properties > Choose the Hardware tab > Look for the COM port under Standard Serial Connection via Bluetooth (COM#) > Make a note of this COM port number.
6. Open AutoResp™ as administrator (right-click).
7. Select the right COM port for this Witrox instrument.
8. Your Witrox instrument is now ready to be used in AutoResp™.

The DAQ-BT device is used for wireless data acquisition from and control of Loligo® swim tunnels. The built-in Bluetooth communication allows you to place the PC at a distance from the swim tunnel. The device has inputs and outputs for controlling and acquiring RPM data from the swim tunnel motor controller (VFC).

Setup

1. To power the DAQ-BT device, connect the DC adapter to a wall outlet and the USB power cable to the threaded socket on the backside of the instrument.
   • Tip: You can power a DAQ-BT instrument directly from your PC using a USB cable.
2. Press and hold the power button until the POWER and STATUS LED flash green. Pairing mode is now enabled.
3. Pairing in Windows 10: Go to Settings > Devices > Add Bluetooth or other device > Choose Bluetooth > Look for BTH-1208LS-XXXX and choose “Pair”.
   • If Windows asks for a pairing code, use “0000” (four zeros).
4. Verify that the DAQ-BT is paired with your PC (under Devices in Other devices list):
   
   
5. Open the program InstaCal (from Measurement Computing) as administrator (right-click).
6. InstaCal will now detect and configure the DAQ-BT instrument (see below). Click OK to the following message:
   
7. Click OK to the following message:
   
8. The assigned board number must correspond to the board number used in AutoResp™:
   
   
9. Click File > Exit
10. If the following error message appears, you must exit InstaCal and open it again as administrator:
    
11. Open AutoResp™ as administrator (right-click).
12. Select the right board number for this DAQ-BT device.
13. Your DAQ-BT device is now ready to be used in AutoResp™.

WARNING: DO NOT reset the device to factory defaults!

Resetting the device to factory defaults will void the warranty and remove the pre-installed Loligo^® firmware leaving the device unable to communicate with any Loligo^® software.

If you have reset the device:

A reset LoligoBT/NETIO4All device must be returned to us for re-installation of Loligo^® firmware. Shipping costs will be charged on your account. Please contact our technical support before shipping anything back.

Ways to reset the device (DON’T!!!)

The LoligoBT/NETIO4All device can be reset to factory defaults in two ways:

1. By pressing and holding outlet buttons 1 and 2 when starting the device via power switch.  Hold the buttons until the device beeps 3 times. During the resetting process, all the outlet LED are blinking red. As soon as reset is completed, the device beeps 3 times. Whole procedure takes about 2 minutes.
2. By removing the protective cap from the ethernet port and connecting the device to a computer with an ethernet cable and resetting the device in your browser.

Contact our technical support if you experience connectivity or performance issue with the LoligoBT/NETIO4ALL. If necessary, we can reset the device for you.

The horizontal mini chambers can be fixed in place in an acrylic holder for easier measurements.

1. Place the acrylic adapter ring in the acrylic holder.
2. Place the mini chamber (with mounted sensor spot on the inside) inside the adapter ring.
3. Rotate the mini chamber so that the sensor spot is located directly below the hole in the adapter ring.
4. While keeping the mini chamber in place, tighten the white nylon screw so that it goes through the adapter ring cutout and onto the glass chamber. Tighten until the mini chamber does not rotate/slide. DO NOT OVERTIGHTEN as it will break the mini chamber.
5. Push the fiber cable through the angled hole in the holder and place cable tip onto mini chamber, so that it is directly above the sensor spot.
6. Tighten red knob to hold fiber cable in place. DO NOT OVERTIGHTEN as it will break the fiber cable.

If the Copy protection error message appears when starting a Loligo^® software, you should check the following:

• That you have inserted the green WibuKey protection dongle (containing the software license) into your computer:
  
• That the green WibuKey protection dongle contains the correct software license and not a license for some other Loligo^® software.
• If you have installed a newer version of the Loligo^® software that you do not have a license for.
  • For software upgrades, please follow this FAQ to update your WibuKey dongle license information.

Acceleration

• The rate of change of velocity per unit of time.

Acceleration X

• The rate of change of velocity per unit of time along the X-axis.

Acceleration Y

• The rate of change of velocity per unit of time along the Y-axis.

AIID

• (Average Inter-Individual Distance) The average of the distances to all other objects:

Bend

• The angle between a line extending through the center of gravity to the back position, and a line extending through the center of gravity and the front position, e.g., use for tail beat frequency estimation:

Direction of movement

• The direction of movement (in degrees or radians) of the position of the animal. The X and Y direction is defined by the user during the Calibration step:

Direction of orientation

• The direction of a line going from the center of gravity position marker to the front position marker of the object:

Distance moved

• Linear displacement of the selected position marker from frame to frame.

Is active?

• Frame to frame object displacement above Activity threshold equals active state (1, in Excel data file) and inactive state (0).

MIID

• (Median Inter-Individual Distance) The median of the distances among all other objects:

NND

• (Nearest Neighbor Distance) The shortest distance to another tracked object:

Raw X or Y Pos

• The raw pixel values of the positions on the X-axis or Y-axis of the selected position marker of the object. X/Y-origin is in top left corner of the frame:

Calibrated X or Y Pos

• The calibrated positions on the X-axis or Y-axis. X/Y-origin is defined during the Calibration step:

Speed

• Linear displacement of selected position marker per unit of time.

Turning rate movement

• The change in direction of movement per unit of time.

Turning rate orientation

• The change in direction of orientation per unit of time.

Velocity X

• The speed of the object in the direction of the X-axis.

Velocity Y

• The speed of the object in the direction of the Y-axis.

This guide will help optimizing your PC for data recording. Note that the optimal settings may vary depending on your PC specifications, and that this guide is based on a modern Windows 10 PC.

Dedicate your PC to data recording

Recording data (e.g., video recording) can be a heavy task for many PCs. Therefore, you should make sure that your computer is focusing most of its processing power on this task. Here are some tips on how to do that:

1. Close all unnecessary software. Ideally, you should only be running your data recording software (and essential Windows processes), so do not listen to music on YouTube or chat in Microsoft Teams while recording data.
2. Prevent process startup. Many processes will start up automatically in the background when you power on your PC. But you can prevent unnecessary processes from doing just that:
   
   
   1. Open the Task manager.
   2. Open Startup.
   3. Right-click on the software (that you do not want to start up automatically)
   4. Choose Disable from the pop-up menu.
   5. Restart your PC.
      
      
3. Go offline. Going offline will prevent many applications from running (also accidentally) during a recording:
   
   
   1. A quick way to go offline is to enable Airplane mode.
   2. Click on the internet icon in the tool bar.
   3. Enable Airplane mode.
      
      
      
      
4. Pause Windows updates. You can pause Windows updates to avoid disruptions during recording. Here is how:
   1. Click on the Windows icon .
   2. Open the Settings menu .
   3. Go to Update & Security.
   4. Go to Windows Update.
   5. Choose the option Pause updates for 7 days.
   6. If you want to resume the updates before the 7 days have passed, click the Resume updates button near the top.
      
      
5. Turn off antivirus. Turning off your antivirus software can free up processing power. Remember to turn it back on again after recording.
6. Fingers off your PC! Once your data recording has started, you should not operate your PC – even moving the mouse curser can lower your PC’s performance!

This guide explains how to set up your camera in the uEye Cockpit software, and how to adjust the typical parameters that is needed to increase your PC’s performance within uEye Cockpit.

Camera setup

1. Connect your camera to the PC. Let it initialize, if necessary.
2. Open IDS Camera Manager.
3. Check that your camera is connected and available:
   
   
   
   
4. Open the Additional functions menu and set the following settings. Click Close when done:
   
   
   
   
5. Open uEye Cockpit as administrator.
6. Make sure that Start uEye Cockpit in expert mode is enabled:
   
   
   
   
7. Choose Monochrome. We generally recommend illuminating your objects with IR backlighting, which is why a monochrome color profile is optimal.
8. Click the Open camera button and let your camera initialize:
   
   
   
   
9. If you cannot see the entire area of interest (AOI) from the camera, click the Scale display to half size button:
   
   
   
   
10. Open Camera properties menu:
    
    
    
    Camera properties optimization
    
    
11. The following settings will maximize your resolution and frame rate for our 4 MP camera. We highly recommend placing the arena on top of one of our IR light panels, and in the center of the AOI. Correct illumination is especially important as it will ensure good video data (e.g., for video tracking):
    
    
    • Under Size, adjust the following settings:
      
      
      1. You can crop your image if your object does not fill out the entire AOI. Cropping the image will lower the resolution but will give a higher maximum frame rate.
      2. Enable Show only AOI.
      3. Profile = undefined
      4. Width = Crop the width of the AOI
      5. Height = Crop the height of the AOI
      6. Left = Adjust to center the object
      7. Top = Adjust to center the object
      8. Subsampling = 1x (for horizontal and vertical)
      9. You may choose 2x subsampling. You will get half the resolution but a much higher maximum frame rate.
         
         
12. Under Image, input the following settings:
    
    
    • Gain = 1.00x (and disable Auto)
    • You can increase the gain value to get a brighter image, but this will add noise to the image.
      
      
13. Under Format, choose the following settings:
    
    
    • Mono 8 (High) (under Software)
      
      
14. Under Camera, adjust the following settings:
    
    
    • Pixel clock. The pixel clock determines how fast the sensor in the camera is being scanned. Higher pixel clock value means higher maximum frame rate, but it will also require more PC/camera performance. The maximum pixel value is defined by the camera and PC performance (bandwidth numbers will be red, if your pixel clock value is too high). We recommend not setting the pixel clock value any higher than necessary to achieve the desired frame rate.
    • Frame rate (Freerun). The frame rate will show you the maximum frame rate achievable at the current pixel clock. You can choose a lower frame rate, but if you want a higher rate, you must increase the pixel clock.
    • Exposure time. The exposure time depends on the currently selected frame rate. You can select a lower frame rate without changing the frame rate. If you want a high exposure time (e.g. to increase the brightness of the image), you need to reduce the frame rate.
    • The values may round up/down to the nearest value.
      
      
15. Achieving a high frame rate is a balance between finding the right resolution and adjusting the camera settings (pixel clock, frame rate and exposure time), so that you get the image you want. The exact settings will vary depending on your PC, camera and camera lens, and physical setup (e.g., lighting).
16. When you are satisfied with your settings, close the Camera properties menu.
17. Open the File menu > Save parameters > to File …
18. Locate a folder where you want to save the current camera properties. This is a time-saver the next time you want to record with the same settings:
    
    
    
    
19. The next time you want to use your saved camera properties with the same connected camera and setup, open uEye Cockpit > File menu > Load parameters > from File … > Locate the settings file.
20. Now you are ready to record a video. Click the Record video sequence button to open the Record dialog:
    
    
    
    
21. Click Create … and choose a file location for your video recording. You should choose a local folder and drive that are not synchronized with any server (e.g., synchronized with Microsoft OneDrive). Usually, your local disk is a good place to save the files: This PC > OS (C:) > Create and use a temporary folder:
    
    
    
    
22. Choose the following settings:
    
    
    
    
    • File: Name of the AVI file opened for recording.
    • Max. Frames: If enabled, you can set the number of frames after which the recording should stop.
    • Maximal [MB): Sets the maximum size for the AVI file. Recording stops when the AVI file reaches the size limit.
    • Current [MB]: Indicates the current size of the AVI file.
    • Received: The number of images transferred by the camera.
    • Dropped: The number of images discarded during compression. An image is dropped if it arrives while compression is in progress.
    • Saved: The number of images saved to the AVI file.
    • Calc. Framerate: If enabled, the frame rate of the AVI file is determined automatically during recording. If disabled, you can input the frame rate that you want to record at. In both cases, the maximum frame rate is determined by your camera settings.
    • JPEG Quality: This slider sets the JPEG compression level (1 = lowest quality, 100 = highest quality, 75 = default).
      
      
23. Click Record. It is important that you do not operate the PC while it is recording – even moving the mouse cursor may lower your PC’s performance.
24. The Missed or Dropped will indicate if your PC or camera is not able to keep up with the camera properties you have selected. Ideally, there should be no lost frames. If you get an undesired number of lost frames, you must lower your camera properties. Note that even though you have set the Calc. Framerate to e.g., 50 FPS, but you get lost frames, the video will not include those frames. This can be deceiving. Yet, the important rule is to notice if there are any lost frames when you stop the recording.
25. Click Stop to stop and save the recording.