What is Live Mouse Tracker ?

LMT is designed to track mice on the long term. It has been created with on idea on mind: to provide behaviourist a reliable system to annotate automatically what mice are doing in their environment, and what are their social interactions. It is fully described in the publication available at bioRxiv. Now published in Nature biomedical engineering.

 

Download

The last version of Live Mouse Tracker can be downloaded here.

Assembly instructions

Download the PDF with assembly instructions here.

How does it work ?

This short video summarize how the system works:

Data analysis

For each experiment, LMT produces a set of data:

  • A database file, in the SQLite format, which is handy as SQLite database are standalone files, which avoid using server. You can just copy/backup/restore/share your databases as easy as manipulating conventional files.
  • A set of video, in the MP4 format, which store the view in LMT. The purpose of those video is to get back to the film if you find specific behaviour while digging in the data. To find back a specific event, we  hard coded in the video the current frame and current date/time. MP4 files are split in 10 minutes segments so that you can play MP4 even during the experiment.
  • A background view folder, which store the depth image of the cage, without the animals. This is great to study how mice are moving objects in the cage, how they organize their nest or how they move/eat their food.

To perform the analysis, we provide a framework in Python detailed in this presentation. We also provide code on GitHub. Examples of data analysis here that contains trajectory drawing, extraction of position, extracting timeline of events. You can also rebuild all the events available using this script. An example of interactive event exploration is also available here.

You can enrich/change the analysis with your own scripts.

Validation

To validate the system (for both the tracking quality and labelling), we annotated manually the following sequence, and we then compared the results to the automatic labelling.

Data sharing

The purpose of this website is to share the data acquired with LMT. Once registered, you can post link to your database, so that others can access and analyse them.

Frequently asked question

How much does it cost ?
The whole system cost less than 2000€. This includes the computer, the RFID antenna/readers, the Kinect v2, the Kinect adapter, cage and tubes. This is a DIY system, assembly instructions are available  here.

Can I track elephant, monkey, bird, ant, spider, flies, mosquito, people, sheep, cow, manta, crocodile, frogs with Live Mouse Tracker ?
No. For those purposes the basics of the method could work, but one would need to switch from a kinect sensor ( accuracy ~1mm and range ~4m ) to a versatile Lidar system. Other tracking exists (and also for mice) and are dedicated to each specific species, and for each existing tracking, they have some requirement and all provides different data extraction.

If I want to track only 1 animal, do I need RFID ?
In that case you don’t need RFID.

On which OS does it work ?
Windows only.

Can I use another computer than the one you recommend ?
We recommend a Ryzen 7 2700X, 16GB RAM. All our systems are working with this kind of computer. It’s up to you to use something else. If we plan to add additional computation to provide better results, we assume that you are using this kind of computer.

Do I need a good GPU / graphic card ?
LMT does not use GPU, you can use any card.

How can I tune the antenna ?
Launch the plugin AntennaTuner in the Live Mouse Tracker tab.

Then in the output of Icy you will see the current tuning refreshed each second.

  • It automatically detects all the COM port as you plug/unplug them.
  • Make the measurement when you are not touching the coil and put the coil far from metallic masses or wires.
  • To increase the value up to 134.2kHz, remove some coil. If you removed more than 10cm of coil, you can cut it and re-solder (note that this will increase a bit the tuning).
  • If you see 0.0 / 134.2kHz it means the wire is broken, or you have a problem with the soldering.
  • To solder the coil, turn it around your wire, and burn (as you solder) the thin translucid isolation plastic that is around the coil.
  • You can also test the detection of your glass RFID probe with the Antenna Tuning Tester plugin. It will cycle through antenna for 5 seconds each, and perform 10 reading per second for each cycle. It will display the RFID number detected in the output.

How much the tuning of the antenna will affect its reading range ?
Robert Warren, from Helmholtz Zentrum München answered this question with this graph (you will use 4.2mm of range per kHz difference with 134.2kHz)

How do I insert the RFID probe ?
The RFID should be gently put in the animal using, using gas anesthesia, and local subcataneous analgesia. The RFID should be inserted in the neck and gently pushed on the side of the animal.

 

Where and which RFID probe should I order ?
You can order probe at https://www.biolog-id.com/

Within a sterile needle (not reusable; it is more expensive, but easier):
TAG_LF_AIG2X12_RO_ISO
TRANSPONDEUR 12MM ISO AIGUILLE STERILE
3.5€ per tag

Without the sterile needle (if you already have an injector and reusable
needles to insert the RFID chips):
TAG_LF_GLT212X12_RW_HTS
TRANSPONDEUR ISO 2.12X12
1.99€ per tag

Can I get back the RFID chip to use them later on ?
You should definitely not. RFID chip are provided with unique number bought by the company which sells it to you. If you do re use number, you will compute databases with several times the same animal, and this will wreck the analysis. Avoid reprogramming the chip with your own number, those number will jam others if you share the database on this website.

Troubleshooting

RFID probe are not detected at all.
Use A+/A- connector on the RFID reader board to connect antenna instead of AR/A-.

Tracks are cut for one frame unexpectedly or images hangs for a few seconds to up to 20 seconds.
This is Kinect related issue. Several solutions are listed here:

  1. Get to Control Panel -> Hardware and Sound -> Sound -> Recording -> Kinect Microphone and enable it.
  2. Open the Microsoft Store Camera app and under Setting -> Change privacy settings -> Microphone -> Allow apps to access your microphone -> enable the microphone.
  3. Some RealTech sound driver seems to create problems (they can consume a lot of memory (more than 1GB) and CPU (1 Full proc). Uninstall those drivers.
  4. The Kinect may be connected on a USB3 that is not fast enough. Connect the Kinect to a USB3 that is on the back of the computer (avoid front panel).