|
ANY-maze Help > The ANY-maze reference > The Protocol page > The elements of a protocol
The elements of a protocol
Introduction
Protocols are divided into a number of different elements, each of which defines a specific feature. There are 54 elements in total, but in the simplest protocol you only have to define six of them. Specifically, the elements are:
Apparatus
The elements in this group define the apparatus in which tests will be performed and the physical equipment that will be utilised.
 Protocol settings | Defines overall features of the protocol such as its name, and most importantly, the protocol mode. |
 Video source | You can add as many individual video source elements to the protocol as you like. Each one defines the video picture of a single piece of apparatus. Generally, you must have at least one Video Source element in a protocol otherwise you won't have any video picture to track in! |
 I/O device | You can add any number of I/O device elements to a protocol; each one defines a specific I/O device you intend to use. This will usually be something like an ANY-maze interface, but it may be the actual apparatus the animal will be tested in, such as an OPAD cage. Anyhow, the important thing is that if you want to read inputs or control outputs, you must include an I/O device element for the device the inputs and outputs are part of. |
 Apparatus | You can include up to 40 individual apparatus elements in a protocol. Each one defines a single piece of apparatus in which you will track animals during your experiment. For example, you could define four activity boxes and then track animals simultaneously in all of them. All protocols must include at least one apparatus element. |
Inputs and outputs
The elements in this group take ANY-maze beyond just tracking animals:
 Synchronisation... | Used to output TTL signals to synchronise tests in ANY-maze with other recording systems. |
 On/off Inputs | On/off input elements can be used to detect things like lever presses or photobeam breaks. |
 Rotary encoders | As the name implies, rotary encoders detect rotations - this might be rotations of a running wheel, or could even be rotations of a tethered animal. |
 Signals | Signals allow ANY-maze to capture analogue data from devices such as ECGs, gas analysers, etc. |
 Sensors | ANY-maze supports various sensors, such as temperature sensors, humidity sensors and weight sensors (i.e. scales). |
 Movement detectors | This element is only included in protocol modes which do not include tracking. A movement detector is able to determine when an animal is moving vs. when it is stationary, without using a video camera. (Note that movement detectors do not track the animal). |
 Output switches | Output switches allow ANY-maze to control devices; for example, an output switch could be used to control a pellet dispenser or a cue light. |
 Speakers | The speaker element provides a way for ANY-maze to play sounds, including fixed frequency tones, white noise, or any sound file. |
 Shockers | Through the shockers element, ANY-maze can control the onset, duration and also the intensity of shocks delivered during a test. |
 Pellet dispensers | Pellet dispensers element allow you to control pellet dispensers during tests. For example, dispensing a pellet as a reward in an operant conditioning experiment. |
 Syringe pumps | The syringe pumps element gives ANY-maze the ability to control the direction and flow rate of a wide range of syringe pumps from manufacturers such as KDS, Harvard and New Era. |
 Analogue outputs | Analogue outputs can be used to control external equipment based on a voltage which ANY-maze generates. The voltage can be directly related to the animal's position, or can be any value based on what's happening in a test. |
 Temperature controllers | As the name implies, temperature controls give ANY-maze the ability to control the temperature of something, for example, a thermal stimulus or the temperature of the apparatus floor. |
 Light controllers | Lighting controllers allow ANY-maze to control the intensity of lights - they're like a dimmer switch that ANY-maze can set. |
Tracking
The elements in this group allow you to set options that control how ANY-maze tracks the animal.
 Animal colour | ANY-maze tracking is essentially automatic - you don't need to set any thresholds or other complex values. Nevertheless, there is one thing the system needs to know - the colour of the animals you intend to track - and you set this here. |
 Tracking options | This element contains various advanced options related to tracking; these won't be required for most protocols. |
Behaviour
The elements in this group are used to specify what behaviours ANY-maze will assess. Here we're using the term behaviour quite loosely, to mean anything that relates to how the animal behaves, including where it goes within the apparatus.
 Zones | You can include as many individual zone elements in a protocol as you like. Each one defines a part of the apparatus which is of interest to you. For example, in a plusmaze the open arms would be one zone, and the closed arms another. You can also define zones which move about between tests and/or between animals, such as an island in a Water-maze or a reward arm in a T-maze. You don't have to include any zones in a protocol if you don't want to. |
 Points | You can include as many points in a protocol as you want. Each one defines a specific position within the apparatus that is of interest to you - for example, the position of a novel object. |
 Orientation and movement | This element is used to specify exactly how ANY-maze determines whether an animal is oriented towards a Zone or Point and whether or not it is moving towards or away from something. |
 Sequences | You can include as many sequence elements in a protocol as you like. Each one defines a sequence of movements around the apparatus which an animal can perform. For example, in a water-maze you could define a sequence to count rotations around the maze and another to count centre crossings. You don't have to include any sequences in a protocol if you don't want to. |
 Immobility detection | In some experiments you'll want to determine when the animal is mobile (i.e. moving from place to place) vs. when it is immobile - this element provides options to do this. It can also be used to determine when animals in Forced swim and tail suspension tests are immobile. |
 Freezing detection | ANY-maze can detect when an animal freezes (no movement except respiration) which, amongst other things, is very useful in fear conditioning experiments. This option allows you to switch freezing detection on and to fine-tune it. |
 Keys | You can include up to 46 key elements in a protocol. Each one defines a key on the computer's keyboard which you can press to register behaviours that ANY-maze can't score automatically. For example, you could define one key to record Grooming and another to record Rearing. You don't have to include any keys in a protocol if you don't want to. |
 Virtual switches | Virtual switches can be used to determine on/off type events based on other information ANY-maze already knows. For example, a virtual switch could be used to determine when the animal is moving faster than a certain speed - when it is, the 'switch' will be on, when it isn't, the 'switch' will be off. Virtual switches can also be used to determine when two or more on/off type events occur - for example, when two specific behaviours detected are both occurring. |
Testing
The testing group elements are used to manage the actual process of performing tests:
 Test scheduling | By default, ANY-maze will use the information you specify in the protocol to automatically build a Test schedule for you. Sometimes this may not be what you want, in which case you can use the option here to manually schedule your tests instead. |
 Stages | All protocols always include at least one stage but you can include up to 45 if you like. Each stage defines a series of trials in an experiment. For example, in a plusmaze experiment, you will probably have a single stage consisting of a single trial, whereas in a water-maze experiment you might have two stages - 'Training', consisting of perhaps 4 trials, and 'Probe', consisting of a single trial. |
Within stages, you can also define stage-end rules. These are rules which can cause a stage to end automatically for an animal (i.e. the animal will have no more trials in the stage). They're particularly useful in 'training' stages; for example, 'choosing the correct arm of a T-maze in 3 consecutive training trials' might be a stage end rule.
 Events and actions |  Events and actions have been replaced by Procedures. They are documented here as they can still be used in legacy experiments. |
Like procedures, events and actions are used to detect certain situations during a test and to take some action when they occur. Specifically, an event determines when something occurs and an action does something because of it.
 Procedures | Procedures are used to detect specific situations during a test and to take some action when they occur. For example, you could use a procedure to end a test when the animal enters the Island zone in a water-maze. Procedures are especially useful with I/O devices, for example, a procedure could determine when an animal presses a lever and decide (based, if necessary, on complex criteria) whether to reward the animal with a food pellet or generate an aversive shock. |
 Automatic starting of tests | When tracking, ANY-maze can automatically start tests when it sees you, the experimenter, leave the camera's view. This element allows you to set up this option. |
 What to record while testing | Obviously, ANY-maze will record a test's results (which include such things as the animal's position), but this element allows you to both fine-tune how often results are recorded and also to optionally specify that tests should be video-recorded too. |
 What to display while testing | While a test is actually running, ANY-maze can show you a wealth of information such as the location of the animal's centre, head, and tail; what zones the animal is in; the state of I/O devices; etc. This element allows you to choose what information you want displayed. |
 Test window panels | ANY-maze uses the Test window panels to display live information while tests are running. There are a range of panels available to show information about Zones, Keys, Inputs and Outputs etc. You can use the options in this element to choose the panels to display and to select the information they should show. |
Additional information
The additional information group provides options to record and utilise additional information about your animals and tests.
 Treatment groups | Allows you to choose whether or not you will organise your animals into Treatment groups and, if you do, to specify how ANY-maze should assign animals to the groups. |
 Animal ID | ANY-maze gives all the animals in your experiment unique identifiers (IDs) called animal numbers. However, your animals probably already have IDs that you use in your lab - the options here allow you to tell ANY-maze that you want to use your own IDs rather than its animal numbers. |
 Treatment doses | If you choose to record the weights of your animals in ANY-maze (see previous item), then ANY-maze can automatically calculate the treatment doses for the animals. |
 Fields | You can include up to 24 different field elements in a protocol. Each one can define a new entry field in which you can record information about individual animals or tests. For example, you could include fields to record the weight or sex of the animals, or to record the light level or temperature in each test. ANY-maze can analyse field entries and can also use them as independent variables in statistical tests. You don't have to include any fields in a protocol if you don't want to. |
Analysis
The Analysis group of protocol elements provide powerful options for analysing the data gathered during an experiment.
 Calculations | You can include as many calculation elements in a protocol as you like. Each one defines a calculation which derives new a measure from those already defined by ANY-maze. For example, in a plusmaze you would probably define an 'Open arms' zone, and this would automatically cause ANY-maze to report a Time in open arms measure. You could then use a calculation to derive a 'Percentage time in open arms' measure from this. |
Calculations can also be used to derive results from multiple tests, for example an average result across a number of trials, or to derive results for segments of a test; for example, distance travelled in the first 2 minutes of a 5 minute test. You don't have to include any calculations in a protocol if you don't want to.
 Time segments | Time segments allow you to divide up a test so you can perform analysis across time. Tests can either be divided into equal duration segments, for example, segments of 1 minute each, or they can be divided into unequal segments which can even be based on the occurrence of something in the test, for example, a segment might start 10 seconds before the animal enters a certain zone and end 20 seconds afterwards. |
By default, all tests will be divided into equal duration segments of 30 seconds and there's no need to do anything if you either don't need time segments or the default setting suits you.
 Analysis | Each protocol always includes a single analysis element, which defines various options related to how ANY-maze analyses test results. |
 Charts | Charts are used to show a plot of some value across time. A wide range of values can be plotted, including such things as the animal's speed, its distance from a zone, the value being read from some I/O device, etc. Charts can be viewed while a test is running (providing live feedback of the value) and can be viewed, copied, saved or printed post-test. |
Reports
The last group of protocol elements allow you to create and adjust the reports and spreadsheets that ANY-maze uses to display an experiment's results.
 Animal details report | This element allows you to fine-tune the information included in the Animal details report, which shows details of all of an animal's tests. |
 Test details report | The Test details report can show a wealth of information about a specific test. This element is used to select exactly what results it includes. |
 Test data report | The Test data report is a spreadsheet which list the actual data collected during a test, such as the x,y coordinates of the animal. This element is used to select the columns included in the spreadsheet. |
 Track plots | You can create any number of Track plots, where each one shows a specific plot (for example, of the position of the animal's head) with specific formatting. |
 Heat maps | You can create any number of Heat maps with each one showing a specific behaviour (for example where the animal reared during a test or where it spent the most time) with specific formatting. |
 Results reports | You can to define any number of results reports - for example, in a plusmaze protocol, you could define a report which would use an ANOVA to analyse the 'Percentage of time in the open arms' between the different treatment groups. |
 Data page | The Data page can show all the results of all the tests in the entire experiment in a spreadsheet format. This element is used to choose which results (columns) should be include and to optionally filter the tests (rows) displayed. |
See also:
© Copyright 2003-2026 Stoelting Co. All rights reserved
ANY-maze help topic T0074
|
Laser controllers
Tracking the animal's head...
Animal weights