Live Mouse Tracker ‐ Assembly - fdechaumont/micecraft GitHub Wiki

LMT Installation Cheat Sheet

Live Mouse Tracker (LMT) is an open-source system for tracking mice using RFID technology and image processing. This cheat sheet provides a concise guide for installing and setting up LMT on a Windows 11 system.

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Live Mouse Tracker
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LMT requirements

4 power outlets (computer, monitor, LMT floor, camera)
workspace of 50 x 90 cm (without computer or monitor)
Windows 10 or later (64-bit)
2 USB 3.0 ports (LMT floor, camera)
LMT structure (camera support, walls, floor)
Optional: +1 USB port for room sensors

System assembly

Dimensions

The LMT system is composed of a floor (the base), walls and a camera structure. The floor has dimensions of 50 x 50 cm, the walls are 50 cm high and the camera is held by a 90 cm structure and placed around 80 cm above the floor. The camera structure is composed of aluminium bars that can be adjusted to fit the camera and ensure its stability.

Instructions

LIVE MOUSE TRACKER Assembly instructions
It contains a detailed description of the system assembly, with schemas, description, list of components and their reference. Use it as a supplementary material to this cheat sheet.

Assemble the aluminium camera structure

The structure is composed of 4 bars (blue values) that are connected with 4 corners (red circles). Both vertical bars and the one at the top are 80 cm long, the two on the ground are 50 cm long.
As an indication, the top bar is placed around 6 cm below the maximum. It can be useful to place it in advance to anticipate the camera calibration step.

When assembling, make sure to center the screw in the slit as shown in the two photos. If not, the screws will not hold both parts together, and the structure may collapse.

Place the camera on the structure

The camera is held in place by two clamps, which allow for easy and precise handling, an essential feature during the calibration process.
Their placement must not interfere with the camera's vertical alignment and should have minimal impact on its orientation. Make sure to align the camera lens with the center of the structure (as shown in the pictures) to save time during the calibration step. A zip tie (also known as ryzlan or serflex) is added as a safety measure to prevent the camera from falling if the clamps fail.

[!IMPORTANT] The support of the camera (where you place the clamps) must be directed towards the front side of the LMT base (the side where cables go out and with the opening to access antennas).

Walls, Wiring and LMT floor

Place the LMT floor in the correct orientation: position the cables on the desired side and ensure the notch for the walls is facing upward. Remove the protective plastic film from both sides of the walls (in the photos the plastic is still present, but you must remove it for accurate tracking).

Arrange the walls as you prefer, ensuring that at least one wall has the holes for the food and water holder. Use the corner pieces to secure the walls together as shown in the picture.
The system is now assembled. You should have two power cables and two USB 3.0 cables (LMT floor and camera). Make sure they interfere as little as possible with the camera's field of view to prevent false detections.

System installation

Windows

Windows 10 or later must be installed on the computer. Make sure all Windows updates are installed to ensure you are running the latest version.

Java

Install Java 8 (64-bit) using Java's website. To verify that the installation was successful, or to check whether Java is already installed, type java -version in Windows PowerShell or Command Prompt. If Java is correctly installed, you should see an output similar to the one shown in the picture.

LMT software

Download the latest version of LMT from the official website (or use this download link). Unzip the folder to the desired directory.

Antennas - MUST BE SKIPPED

[!IMPORTANT] Antennas are usually already configured, so you must skip this step to avoid errors.

Ensure the LMT floor is connected to the computer. Go in Device Manager (in french: Gestionnaire de périphériques). All 16 antennas should appear as FT232R USB UART or USB Port COM. All necessary drivers are installed automatically. Wait until all antennas are listed as USB Serial Port (COM …) in the Ports COM section.
Turn off all antennas, then turn them on one by one. Rename them sequentially to the correct COM ports (from 30 to 45).
Start LMT using Live Mouse Tracker.bat (you can also use icy.exe, but this is not recommended).
In the software, go to Live Mouse Tracker >> LiveMouseTracker >> Antenna Setup.
Click on Set antenna serial number, then Read antenna serial number. Repeat until all antennas are correctly configured. When clicking on LiveMouseTrackerCalibration, the numbers after "tuned to ..." must be strictly positive. If any number is zero, the antenna may be unsoldered or have other hardware issues.

Final adjustments

Camera calibration

In the Calibration section, multiple numbers are shown on the live image. Adjust the camera position to match those criterias:

the big yellow square match the walls' base
all numbers are green or yellow (between 610 and 650)

Those criterias correspond to an appropriate height of the camera, and a parallelism between camera and LMT floor.
For a proper image, a piece of tape must be placed on the camera to hide one of the 3 blasters. This will remove the areas that are too illuminated in the scene (white pixels). See the green tape on the picture for help.

LMT configuration

In the Live Mouse Tracker folder (the one you previously downloaded), open the lmt folder. Inside, there are some .xml files. The file lmt-config.xml is the configuration used by the software. It must be replaced according to the experiment.

As an example, for a classical mice experiment, do the following steps:

delete lmt-config.xml
duplicate lmt-config - block 50x50 with walls.xml
rename the copy into lmt-config.xml

Room sensors - can be skipped

To set up the room sensors, connect the device to the computer. In Windows Device Manager (in french: Gestionnaire de périphériques), rename to COM port 29 the corresponding device in the Ports COM section. Now, when LMT is on, all room sensor values must appear on the screen.

[!NOTE] If you do not set up the room sensor device, LMT will still work perfectly.

Congratulations

LMT is now functional! To start an experiment, go to Live Mouse Tracker >> LiveMouseTracker >> Start Live !.

Data outputs

Datasets generated by LMT are stored in different formats, depending on the type of data.

SQL database

LMT generates a SQLite database file for each experiment. This file contains all the tracking data, including the room sensors data, the time and frames and all animals information (ID, RFID, position) and behavioral events. It can be accessed using any SQLite viewer like DB Browser or programmatically using libraries such as sqlite3 in Python.

Video & image recordings

LMT generates background images such as video recordings of the experiment. These videos are stored in MP4 format in the same directory as the SQLite database files. They can be viewed using any media player that supports MP4 format, such as VLC Media Player or Windows Media Player.

Data analysis

For a generic analysis of the LMT database, you can use the Live Mouse Tracker - Explore Your Experiment application LMT-EYE that provides a graphical interface for visualizing and analyzing the data. Many other tools to analyse your LMT data have been developped by users, you can find some on the LMT official website. For more advanced users, custom analysis can be performed using programming languages such as Python. You can ask on the LMT Discord channel for help with data analysis and to share your scripts with the community.