Getting Started

This page describes how to set up the µLogger device and explains what is shown on the display of the µLogger brain. If you are already familiar with this, you can jump straight to the µLogger GUI.

Powering up the µLogger brain

Connect the 24V power supply to the back of the rectangular µLogger controller box (the "brain").

The µLogger brain will power up (takes 2-3 seconds), briefly show the version of the µLogger software running on the controller, and then switch to the following view with the name of your µLogger in the upper left corner (this uniquely identifies this particular brain), and a warning triangle and wifi symbol in the upper right corner. The warning triangle is display because the "brain" is not connected to a reader yet (hence the "connect to reader" message on the screen), and the wifi symbol indicates whether the brain is connected to the internet. Once the µLogger brain successfully connects to the internet (via Wifi), the wifi symbol will switch to the wifi symbol without the line through it (right). The brain may connect to the internet so quickly that you never actually see the crossed out wifi symbol shown on the left.

The brains have magnets embedded in the top and bottom so you can easily attach them to any metal surface or stack them on top of each other. Place them in a location where they are easy to see so you can check on your experiments on the fly (outside wall of incubators is a favorite for us). Do not place the brains inside an incubator as this may interfere with their internet connection (and makes it pointless to have the brains separate from the µLogger devices in the first place). Just run the connecting network cable from the brains to whereever you want to place your actual cultures (e.g. inside an incubator).

Connecting device to brain

Connect the µlogger device to the brain with a standard network cable (any length works but we generally recommend cables < 20 meters to avoid potential signal interferences for the OD measurement). Once connected, the display on the brain will switch to one showing the device status, which typically looks something like the below (default µLogger settings on the left, fully configured µLogger on the right).

Note that you can connect/disconnect µLogger devices at any time (including before powering up the brain). The settings are stored in the brain (not on the device) and will be transmitted to whichever device gets connected. However, powering down a brain (on purpose or from e.g. a power outtage) will reset all µLogger settings to the last saved state. However, any saved state IS preserved across power outtages and the µLogger will simply resume where it left off after power cycling. How to change µLogger settings and saving device states is explained in detail on the Device Control page but we recommend you follow this Getting Started guide until we get to that page.

What do the different display lines mean?

• Line 1: this line shows information about the OD reader
  • left: if the OD reader is not zeroed, this shows the light detector saturation (in ppt from 0 to 1000), example: SAT: 734; if the reader has been zeroed, is shows the optical density, example: OD: 0.234
  • right: shows status messages for the OD reader, examples: zero me (indicating the device has not been zeroed), or in 1m30s (a countdown indicating the next OD reading will happen in 1 minute and 30 seconds)
• Line 2: this line shows information about the stirrer
  • left: shows the current speed of the stirrer, e.g. RPM: off (stirrer is off) or RPM: 500 (stir speed is currently 500 rotations per minute, measured by a rotation feedback sensor)
  • right: shows the setpoint for the stirrer, e.g. SP: 500rpm (target stir speed is 500 rpm), if the stirrer is turned on, this is the speed the device tries to match as close as possible
• Line 3: this line shows information about environmental parameters
  • left: the voltage of the power supply, this should be close to 24 V - the µLogger does not work if the voltage is too low (~ 20V) and a much higher voltage can damage the stirrer motor and optical density sensor
  • right: the temperature inside the µLogger device, this sensor is very precies but may not be 100% accurate without offset calibration - regardless, it should show a temperature close to ambient (e.g. the temperature set inside the incubator where the µLogger is located) and remain stable over the course of an experiment if the external temperature is held constant
• Line 4: this line shows information about illumination (needs the phototroph adapter module)
  • left: shows the current light intensity from 1% to 100% (or off if illumination is currently off)
  • right: shows the illumination setting, e.g. always off means illumination is disabled, always on means illumination is always on at the set intensity, off:5h30m means illumination is on a schedule and the light will turn off in 5 hours and 30 mins (on:1m20s would mean it turns on in 1 minute 20 seconds)
• Line 5: this line shows information about air cirulation (needs the phototroph adapter module)
  • left: shows whether the fan on the phototroph adapater module is currently on or off - the fan is designed to make sure the area around the culture vessel is well ventilated to reduce the temperature effects of illumination (even LEDs generate some heat)
  • right: whether the fan is always off, always on or turns on and off together with the illumination (with light)
• Line 6: this line shows information about data transmission (called Publishing or sometimes Recording)
  • off indicates that no data is transmitted by the device, in 12m means that the next global data transmission happens in 12 minutes, i.e. all sensor data that is averaged over the publish interval such as temperature, voltage, stir speed, OD, etc. will be sent to the database at that point (with an average, standard deviation, and number of measurements). The device publishing is turned off/on by the experiment recording settings in the Experiment Configuration, the publish interval can be adjusted in the Device Control. To make it easy to see if a µLogger is currently publishing the data it collects, the hard disk with up-arrow symbol in the upper right corner of the display indicates the current publishign status.

Finally, if you ever still see the warning triangle (brain screen upper right corner) AFTER a device is connected, it means that there is a problem with the stirrer motor or one of the sensors. Look for error messages shown on the brain display or in the Device Control and check the Troubleshooting guide. For example, one error you may encounter indicates that the OD sensor is saturated (see example below). This means that the gain amplification of the light sensor is too high and the current light intensity saturates the OD detector. This can happen if you switch from a large culture vessel (e.g. a serum bottle) to a narrow culture vessel (e.g. a culture tube) which focuses the light beam more intensely but the detector has not yet been re-zeroed. See Device Control for how to zero your µLogger (always do this at the beginning of a new experiment!).

Changing device adapters

The µLogger base (pictured above) is compatible with a number of bottle adapters ranging in size from small 15mL culture tubes (sometimes called Hungate tubes) to large 160ml serum bottles (examples shown below). These are magnetically attached to the µLogger base and can be easily swapped between experiments with different culture bottle sizes. We have a number of sizes already designed (see latest list) but since these are scripted 3D-printer parts, it is easy to make and 3D-print adapters for any bottle size with outer diameter < 57mm (wider bottles do not fit inside the µLogger base anymore). Just reach out if you're looking for something we don't have yet.

When swapping adapters, make sure that the adapter sits snugly in the groves of the µLogger base and does not move, otherwise your culture vessel may move during an experiment and OD readings become less precise. Likewise make sure that the spring-loaded core of the adapter you are using fits your culture vessel snuggly. This makes sure the vessel stays centered in the light absorbance beam during your experiment. If you are using relatively small culture vessels (e.g. standard 25mL culture tubes), make sure to use an adapter insert (picture below) that clips into the bottom of the µLogger base (it can optionally be screwed in with M3 machine screws but this is usually not necessary). This base adapter ensures that the bottom of your culture vessel does not touch the magnetic stirrer, which can lead to misalignment and imprecise OD measurements. Bottles with diameters larger than the µLogger base stirrer (29mm) do NOT need this precaution as they sit safely on the edges of the µLogger base. In fact, do NOT use the clip-in base adapter with larger bottles so that they stay as close as possible to the stirrer for optimal magnetic coupling.

If you are growing phototrophs and want to use the µLoggers' light control functionality, simply attach one of the light adpaters ON TOP of the culture vessel adapater. They are held in place with the magnets that line up with the culture vessel adpaters underneath. Any light sheet can be glued into the adapters but we typically use 24V white color Auragami light sheets which work great for cyanobacteria and algae (about 4mW per LED). Simply connect the cable from the light sheet to the Light port on the µLogger circuit board and the fan cable to the Fan port to control illumination and fan through the micrologger brain/web interface.