behaviorMate is an Open Source package for collecting time-stamped behavior data during animal experiments. It provides:
- A user interface for adjusting experimental parameters and viewing its current state
- Asynchronous communication with actuators (reward valves, tone generators, etc.) and sensors (rotary encoders, capacitance sensors, etc.)
- Time-stamped logging to a TDML file
If you use behaviorMate for your research, please cite the following paper in any resulting publications:
Windows 10/11
Option 1: Download prebuilt jar
- Download zip: behaviorMate.zip
- Extract the behaviorMate folder.
Option 2: Download and build from source [Windows]
- Clone the repository:
git clone [email protected]:losonczylab/behaviorMate.git - Install Chocolatey package manager and make
- Open PowerShell as administrator and run the following commands:
Set-ExecutionPolicy Bypass -Scope Process -Force; [System.Net.ServicePointManager]::SecurityProtocol = [System.Net.ServicePointManager]::SecurityProtocol -bor 3072; iex ((New-Object System.Net.WebClient).DownloadString('https://community.chocolatey.org/install.ps1'))choco install make - Navigate to the behaviorMate root project directory containing the "make" file. Then run:
make all
To start the application simply open the BehaviorMate.jar file using your Java 8 installation.
After launching BehaviorMate, a file selector will pop up for choosing the desired settings file. If the settings file is invalid, the file selector will pop up again. If the selector is x'd out, the program will terminate.
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Fill out the "Project Name" and "Mouse Name" fields. The trial will not be able to start until these are filled.
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2a) Treadmill only: hit the "Calibrate" button and move treadmill manually by hand until the lap reset bar turns white on lap completion and the desired error is achieved. Add the new position scale to your settings file.
2b) VR only: hit the "Reset" and "Zero" position buttons. Filling out trial data fields
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Start will start the trial. After hitting Start, the Stop button will appear. After clicking Stop, you will have the option of Saving or Deleting the collected behavior data. If saved, the data will be written to a TDML file.
The settings file is what you will use to configure BehaviorMate to run your experiment. The default settings file BehaviorMate will look for is settings.json in the root project directory. However, any properly configured JSON file in any directory may be used. Example settings files and a discussion of their components are presented in main figure 2. Note: not all possible options and configurations are present in figure 2 (// may want to have a comprehensive cheat sheet for all possible properties). One of the most important aspects of the settings file are Context Decorators. These are what you will use to set up the "events" of your experiment such as releasing an odor at certain times, providing a water reward at certain locations in the track, etc. The decorators simply control the conditions in which a Context will be enabled. The Context Decorators have no knowledge of the underlying Context they are managing and work for any Context. Context decorators should not wrap other context decorators, as the resulting behavior can sometimes be unpredictable. Instead, it is encouraged that you create your own decorators for more intricate experiments since creating decorators is fairly straightforward.
This is a brief explanation of each decorator class and how to use this class in the settings file. These are referred to in the settings file by removing "ContextDecorator" from the name (Ex: AlternatingContextDecorator = Alternating).
AlternatingContextDecorator -Used to disable the Context every certain number of laps.
BlockedShuffleContextDecorator - Used to place the Context randomly along a certain section of the track.
DelayedContextDecorator - Delays the Context from being enabled until a certain amount of time has passed after the start of the trial.
JointContextDecorator - Allows a group of Contexts to be enabled and disabled together. Provides options to allow Contexts to be enabled a certain amount of time or certain distance after another Context (Ex: Enabling an odor Context 0.5 seconds after a lick Context has been enabled).
RandomContextDecorator - Used to enable the Context every random number of laps. It is disabled otherwise.
ScheduledContextDecorator - Used to disable the Context on certain laps and it is enabled otherwise.
TimedITIContextDecorator - Used to disable the Context for random amounts of time before it is re-enabled.
Context - a feature of the mouse’s environment. The feature can spatial or temporal. Some 467 context decorators may make use of both simultaneously, such as a custom decorator that 468 gives a reward in the second half of the track every other minute or lap. A context is made 469 up of subcontexts (see below). The number of subcontexts is set by the location parameter 470 (maybe should be renamed subcontexts) in the settings file. 471
Subcontext (May want to call this an Event) - Take a random context decorator with 4 locations 472 of radius 50. When the mouse enters any of the 4 random blocks, it will be given a reward. 473 Each of these blocks can be thought of as a subcontext. 474
Context List - probably don’t need to talk about this. Seems relevant only for code 475
Context Decorator - In the source code, a Context Decorator will wrap a Context List and 476 provide additional functionality. This is what the user will implement to get behaviormate to 477 provide the desired functionality. 478
Spatial Field - the spatial field of a subcontext is the section of track it encompasses. The 479 spatial field begins at LOCATION-RADIUS and ends at LOCATION+RADIUS. If the mouse’s 480 position is greater than LOCATION-RADIUS and less than LOCATION+RADIUS, it is said to 481 be in the context. The mouse is in the spatial field of a context if it is in the spatial field of any 482 of its subcontexts. 483
Temporal Field - temporal field of a subcontext is either the time or set of laps during which 484 the Context (and all of its subcontexts) will be enabled. For an alternating context with n=2, 485 the temporal field is the set of all even-numbered laps. For a delayed context decorator with 486 delay=6, the temporal field includes the span of time starting at 6 seconds and going to infinity. 487
Enable (alternate terms: active) - A Context is enabled on a given lap or at a certain moment 488 in time if when the mouse enters its field, some sort of reward or stimulus will be given. A 489 context is enabled unless the implemented decorator causes it to be Disabled under certain conditions. For example, an alternating context decorator Disables the wrapped context every 491 certain number of laps.
Disable - A Context is disabled if even when the mouse is in its field, no reward or stimulus 493 will be given. 494
Trigger - A Context is said to be triggered if it is 1) enabled and 2) one of its subcontexts has 495 been triggered. A subcontext is triggered when both its spatial (mouse is in the right location) 496 and temporal (the time is right) conditions have been met. A subcontext cannot be triggered if 497 the Context it is a part of is not enabled.
Unless otherwise specified in individual files, all code is Copyright (C) 2023 The Trustees of Columbia University in the City of New York.
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