ANY-maze Help > The ANY-maze reference > The Protocol page > The elements of a protocol > Apparatus > Protocol settings > The protocol mode
The protocol mode
Introduction
The protocol mode alters how ANY-maze operates. It does this in three ways:
| • | It limits the protocol elements included in the protocol list to those which are relevant to the mode in use. For example, when Input/Output only mode is selected, all the protocol elements used for video tracking are removed. |
| • | It adjusts the features available within ANY-maze depending on the type of licence you own. |
| • | It provides short-cuts to building protocols for ANY-maze specific equipment |
Figure 1. The protocol mode list. Modes are grouped into four categories, clicking a category title opens it to show its modes.
Full details about the protocol mode are given in the sections below:
| • | The different protocol modes |
| • | Setting the protocol mode |
| • | How should I choose which protocol mode to use? |
| • | How licences affect the available modes |
The different protocol modes
There are six Standard protocol modes, three TakeNote modes and various Equipment-specific modes.
Standard modes
| Video tracking mode | This is the default mode, and provides all the features needed to video-track animals within your apparatus. |
| Video tracking mode with input/output | This is the most complete mode and enables all the features of ANY-maze, including those used to interface to input/output devices, such as photobeams, shockers, etc. This mode is appropriate when you not only want to track the animal within your apparatus, but also want to record the input from some type of I/O device, such as a micro-switch or photobeam, and/or control some sort of output such as a speaker, shocker, lamp etc. |
Note that in Freezing detection mode you will still be using video, and so you will still need to set up Video sources and you will still need to include Apparatus items in your protocol. You will also need to draw the outline of the apparatus map, so ANY-maze knows where in the video image it should be detecting freezing. When you perform tests in this mode, ANY-maze will show the video image of your apparatus (although it won't track the animal).
This mode is similar to Video tracking mode except that the definition (and detection) of immobility is specific to these tests (i.e. it is different to the immobility reported when animals are normally being tracked). For example, in the FST it ignores drifting and the small movements necessary to keep the head above water, while in the TST it ignores swinging. You can learn more about this immobility detection here.
This mode also excludes other features from the protocol, for example head tracking is unavailable, as are Sequences.
When a protocol is using this mode, all options related to video and video tracking will disappear from the protocol list - this includes Video sources, Zones, Points and Sequences.
Note that in this mode you will still need to create Apparatus items in your protocol, although you won't have to select a video source for them. During testing, ANY-maze won't show a video picture of your apparatus; in its place it will show the state of the various inputs and outputs included in your protocol.
| Operant mode | This mode is designed for use with the ANY-maze Operant Interfaces, which provide a straightforward way to connect ANY-maze to Operant cages from Med Associates, Coulbourn Instruments and Lafayette Instrument. |
This mode makes it very easy to add operant cages and the components in them (such as levers, pellet dispensers, etc.) to your protocol. This mode also supports sub modes.
TakeNote modes
In the TakeNote modes, ANY-maze does not track the animal; rather you will observe the animal and score its behaviour using keys.
| TakeNote video observation mode | In this mode, ANY-maze will not track the animals in the video picture of the apparatus; rather, you will use keys to score the animal's behaviour manually. This mode is appropriate when you either don't care where the animal is within the apparatus (because you just want to score what it is doing), or your apparatus is such that the video tracking won't work. |
When a protocol is using this mode, options that require video tracking will disappear from the protocol list - this includes Zones, Points and Sequences as well as the options to detect immobility and freezing, and those to track the animal's head and to automatically start tests. Furthermore, you won't need to draw any apparatus maps, but all other features of ANY-maze will still be available.
Note that in TakeNote video observation mode you will still be using video, and so you will still need to set up video sources and you will still need to include Apparatus items in your protocol. When you perform tests in this mode, ANY-maze will show the video image of your apparatus (although it won't track the animal) and you will be able to press keys to score behaviours manually.
TakeNote video observation mode with input/output
This is similar to the previous mode, except that features used to control input/output devices, such as photobeams, shockers, etc. will be available. This mode is appropriate when you want to both observe the animals and record data from inputs and/or control outputs.
| TakeNote direct observer mode | This is similar to the TakeNote video observation mode except that you won't be observing the animal in a video picture, but rather observing it directly (i.e. you'll be looking directly at the animal). In this mode, all elements relating to video and to tracking will disappear from the protocol list - this includes Video sources, Zones, Points, etc., but you will still need to include Apparatus items in your protocol (the apparatus being where the animal that you're observing is). |
This mode is appropriate when you want to observe animals without using video - for example, you might just be sitting in a lab watching the animals in a cage, or you could be observing them in the field.
Equipment-specific modes
As the name implies, the equipment-specific modes are used with specific pieces of equipment, such as the OPAD cage.
ANY-maze includes various Equipment-specific modes such as OPAD cage mode and RAPC mode. These modes are usually selected automatically based on your ANY-maze licence.
As well as limiting the elements included in the protocol, these modes also make it easy to build your protocol because the system knows the features that the equipment provides. For example, an OPAD cage includes (amongst other things) two touch switches, one of which is activated when the animal makes contact with the 'thermal elements' and the other when it licks the spout of the water bottle. Because ANY-maze knows this, it means that when you add an OPAD cage into your protocol, the system can automatically include appropriate on/off inputs for these items.
In fact, the equipment-specific modes not only automatically build the protocol, but they can also cause the protocol to include some elements which are only relevant to the equipment whose mode is chosen. For example, when an OPAD cage mode is selected, the Analysis element of the protocol includes a sub-element for Analysis of OPAD results.
As mentioned above, the equipment-specific modes limit the elements included in the protocol to those that are relevant to the specific equipment. However, you may encounter situations in which you want to use other features of ANY-maze in an equipment-specific mode - for example, you might want to track the animal within the OPAD cage, but this won't be possible because all the protocol elements related to tracking will have been removed from the protocol. There is, however, a solution to this: if you own a full or I/O only ANY-maze licence, then when you select an equipment-specific mode a second list will displayed where you can select a sub mode. The sub modes allow you to switch on additional features of ANY-maze whilst remaining within the equipment-specific mode - for example, you can remain in OPAD mode, but switch on the features for video tracking. Further details about sub modes are given in the next section.
Setting the protocol mode
To set the protocol mode, you should first select the Protocol element in the protocol list (it's the first item) and then select the mode you want from the list shown in the Settings pane.
The default mode, which ANY-maze will select automatically when you create a new protocol, will depend on your ANY-maze licence. For example, if you own a licence for the OPAD cage, then the default mode will be OPAD cage mode. On the other hand, if you own a TakeNote licence, then the default mode will be TakeNote video observation mode. But it's most likely that you own a Full licence (or no licence, because you are trialling ANY-maze) in which case the default mode will be Video tracking mode.
To change the mode simply select a new mode from those shown. You may find that some modes are disabled; this means that your licence doesn't allow you to use those modes. For example, if you own a TakeNote licence, then the Video tracking modes will be disabled.
While you are designing a protocol, you can change the mode at any time. So you might start off intending to use Input/output only mode but then decide that you would like to track the animals too, and so change to Video tracking mode with input/output. However, after you start the experiment - that is, after you have performed at least one test - you can no longer alter the mode. This is a hard rule and there is no way to work round it.
Sub modes
If you own a full or I/O only ANY-maze licence, then when you select Operant mode or an equipment-specific mode, a second list will displayed where you can select a sub mode. The options shown can include:
| • | Standard sub mode |
| • | I/O sub mode |
| • | Full sub mode |
 | WARNING: Changing the sub mode causes the protocol to be cleared - that's to say, all the entries in the protocol are deleted - so it's a very good idea to select the correct sub mode before you start setting up the rest of the protocol. |
Standard sub mode
This is the default sub mode, and will cause the protocol to only include the elements that are required to use the relevant equipment. For example, if you are using OPAD thermal mode, then the standard sub mode will include protocol elements for On/off inputs, Temperature controllers, etc. as these are inputs and outputs that OPAD includes; but it won't include such things as On/off outputs, Zones or Points, as these aren't required to run OPAD tests.
This sub mode is the best one to use if your experiment doesn't actually require any of the extra features that the other sub modes provide, as it keeps the protocol simpler.
I/O sub mode
In this sub mode, all the input/output elements are included in the protocol. For example, normally when using an OPAD mode, the protocol will include some input/output elements (being those that are required for OPAD) but it won't include such things as on/off outputs, signal inputs, syringe pumps etc. Selecting the I/O sub mode changes this, so that all the input/output elements are included, allowing you, for example, to use a syringe pump with OPAD.
This sub mode will only be available if you have a full or I/O only ANY-maze licence.
Full sub mode
In this sub mode, all the protocol elements are available. This means that you can use all the features of ANY-maze. For example, if you are using OPAD mode, then selecting this sub mode would allow you to use any input or output, to track the animal, to detect freezing, etc.
This sub mode will only be available if you have a full ANY-maze licence.
How should I choose which protocol mode to use?
If you own a full licence for ANY-maze, then all the protocol modes will be available to you, so how should you choose the one to use? The answer depends on what you're trying to do, but there are a couple of simple rules you can apply:
| • | Choose a mode which includes all the features you need. This sounds rather obvious, but clearly, if you want to track your animals then you must use one of the Video tracking modes. |
| • | Choose a mode which only includes features you need. This is a little less obvious, but consider this scenario: You want to score how often an animal in a Skinner box presses a lever; which mode should you use? Well, you need an input so applying the first rule, you will need a mode that includes Input/Output. But there are four of those, so which of the four should you use? Applying this rule you would choose the Input/output only mode, because you don't need to track an animal or detect freezing (features the other modes provide). It's useful to understand why this is important: consider what would happen if you chose the Video tracking mode with input/output - ANY-maze would expect you to track the animal, so it would expect you to set up a video source, draw an apparatus map, etc., but as your apparatus doesn't include a camera, you wouldn't be able to do this. |
Of course there's one other rule - if you're using a piece of equipment which has its own mode, such as an OPAD cage, then you should use the equipment's specific mode.
As mentioned above, if you own a full or I/O only ANY-maze licence, then when you select an equipment-specific mode, you will have the option to choose a sub mode too. You should choose the simplest sub mode which provides the features you need for your experiment, as this will make the protocol simpler. For example, if you don't need any additional input/output (over and above that which the equipment itself provides) then you should choose the Standard sub mode. However, if you need some additional inputs or outputs then you should choose the I/O sub mode, and only if you need to track the animals should you choose the Full sub mode.
How licences affect the available modes
As you probably know, to actually record the results of tests performed in ANY-maze, you need an ANY-maze licence. The most common licence is a 'Full licence' which causes all the protocol modes to be available. But there are also (cheaper) licences available such as the 'TakeNote' licence, which makes the TakeNote modes available but which won't allow you to select any of the Video tracking modes.
Some ANY-maze licences are apparatus-specific; for example, the OPAD cage is provided with a copy of ANY-maze, but the licence is specific to the OPAD cage. Similarly, the RAPC apparatus is provided with a RAPC-specific licence. These licences only enable their respective Equipment-specific modes.
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