ANY-maze Help > Using ANY-maze > Setting up an experiment > Creating a new protocol for an experiment

Creating a new protocol for an experiment

If you're going to use a new piece of apparatus in an experiment, or if you're just starting out with ANY-maze, then you'll need to create a new protocol from scratch. Although this can seem rather daunting, it's usually quite simple and in this topic, I'll lead you through the steps you need to take.

Before you start, it's a good idea to read the Introductory tutorial on protocols which will help you to understand the structure of a protocol and how they work.

The key to setting up a protocol, at least while you're unfamiliar with them, is to work through the protocol list from top to bottom, visiting each item and reading its description. You'll probably find that many of the elements won't be required in your protocol, but at least this way you won't miss anything.

The rest of this topic highlights the elements you would typically use when creating a simple video tracking protocol, for apparatus such as the plusmaze or water-maze.

   Setting up the protocol element itself   (Compulsory)

All protocols include a protocol element which defines such things as the protocol's name and the protocol mode. Full details can be found in the Protocol settings topic, but suffice to say that the protocol mode is quite important as it controls the elements available in the protocol list. You should choose a mode appropriate to what you want to do, which for standard video tracking would be the default Video tracking mode.

   Setting up the video source(s)   (Compulsory)

You have to include a video source in all protocols (which use a video protocol mode) because this is what provides the video picture of your apparatus - no picture, no tracking!

The comprehensive introduction to video sources is well worth reading if you're not sure what video sources are all about.

If you're planning to test in a single piece of apparatus which is viewed by a single camera, then setting up the video source should be very simple, but here are some notes about more complex situations:

   Creating the apparatus element(s)   (Compulsory)

Once you've set up your video source, you will need to create the apparatus element which will actually represent your apparatus in the protocol.

Apart from naming the apparatus and selecting the video source which shows it, the most important part of setting up the apparatus is drawing the apparatus map. This map actually indicates to ANY-maze what parts of the video picture constitute the apparatus, and also serves to divide the apparatus into different areas.

The final task to perform here is to use the ruler line to define the scale of the apparatus map.

   Dividing the apparatus into zones   (Optional)

In many experiments you will want to divide your apparatus into different areas - the open and closed arms of a plusmaze for example - and this is what zones are for.

   Defining points within the apparatus  (Optional)

In some apparatus, you might be interested in specific points - for example the centre of a novel object. If you include a Point in your protocol, then ANY-maze will report such things as the distance from the animal to the point, the time the animal spent moving towards the point, the time moving away from it, etc. Of course, you can include as many different points as you like.

   Measuring sequences of movements   (Optional)

Apart from just measuring information for specific zones in the apparatus, you may wish to measure movements between different areas. For example, you might want to find out how often the animal walks across the centre of an open field, or how many spontaneous alternations it performs in a Y-maze. This type of analysis is performed using sequences.

   Specifying the colour of the animals to track   (Compulsory)

ANY-maze only requires one piece of information about your animals in order to track them, and that's whether they are lighter or darker than the apparatus background. As well as options for lighter and darker there are also options you can use for non-uniform animals (or background) and for when you'll be using different coloured animals in the same experiment.

   Using keys to measure other behaviours   (Optional)

Clearly there may be behaviours you would like to score during tests that ANY-maze can't detect automatically; grooming for example.

To resolve this issue you can define keys on your computer's keyboard for up to 40 such behaviours, and simply press the appropriate key while a behaviour is occurring - irrespective of where in the apparatus the animal is.

ANY-maze will automatically analyse such behaviours for the apparatus as a whole, and also for each of the zones individually. For example, in a plusmaze it could tell you the overall time spent grooming as well as the time spent grooming in the open arms and time spent grooming in the closed arms.

If you're testing in more than one piece of apparatus simultaneously, then you can still use keys but you will need to define a different key for each behaviour in each piece of apparatus - for example G might be grooming in Plusmaze 1, and L might be grooming in Plusmaze 2.

   Setting up the experiment's stages   (Compulsory)

In many experiments, particularly those related to memory, you will want to test animals more than once. For example, in a water-maze you might train animals to find a platform, treat them and then retest them to assess the effect of a treatment. In this case your experiment would have two stages - Training and Retest.

In fact, in all experiments you must define at least one stage, otherwise the experiment won't include any tests at all. So, for example, a plusmaze experiment would include a single stage, probably consisting of a single test.

   Using procedures to automatically perform actions while a test is running   (Optional)

In some experiments, you may wish to detect when something happens and take some action because of it. For example, in a water-maze you'd probably want to detect when the animal finds the island, and then end the test. ANY-maze uses procedures to do this. A procedure is a series of instructions which ANY-maze will perform while a test is running. One of the most useful instructions is 'Wait until', which causes the procedure to wait until something occurs (perhaps the animal entering the island zone) before it moves on to perform the next instruction (which might be to end the test). Here's how that procedure would look:

Wait until: Animal enters Island zone

Action: End the test (Reason: Found platform)

   Specifying how animals get assigned to treatment groups   (Compulsory)

In ANY-maze experiments, you will typically divide animals into different treatment groups. However, you don't have to do this, and you can use the options in this element to choose whether to use treatment groups or not and, if using them, how the animals should be assigned to their groups. You have to make a selection and full details of the options can be found in the Treatment groups topic.

   Recording the animals' weights   (Optional)

In many experiments you will want to record the animals' weights, so ANY-maze includes a specific option for this. You can choose whether you'll record the weights just once or multiple times (perhaps before every trial the animal has), and how you'll weigh them, either manually or using the ANY-maze animal scales (which have the advantage that the weights are automatically recorded by the software). Full details of the options can be found in the Animal weights topic.

If you do record your animals' weights, then you can also optionally choose to have ANY-maze calculate treatment doses too - further details can be found in the Treatment doses topic.

   Using fields to record additional data about animals or tests   (Optional)

It's quite common to need to record additional data in an experiment, such as the water temperature in water-maze tests. Although you can obviously note this information on paper, there are advantages to using fields within ANY-maze to record it.

If you define a field in the protocol, ANY-maze will include places for you to record the relevant data against each animal or test in the experiment.

Some of the advantages of using fields are:

   Using calculations to derive new measures   (Optional)

ANY-maze automatically includes many measures such as times in zones, distances travelled etc. However, you may want to derive new values from the ones supplied, and this is what calculations are for.

For example, in a plusmaze it's common to report the percentage of time spent in the open arms. ANY-maze doesn't automatically include this measure, but you can easily derive it from those it does include by defining the calculation:

  (Time in open arms / (Time in open arms + Time in closed arms)) * 100

Calculations can also include functions which, amongst other things, can be used to extract results from parts of tests - for example, the first 3 minutes of a 5 minute test - and to calculate results across tests, such as the average distance travelled in all the tests of a particular stage.

   Specifying how ANY-maze should analyse results across time   (Optional)

ANY-maze can automatically break tests up into segments (sometimes called 'Time bins') and report results for each segment individually. This can be very helpful when you want to see how the animals' behaviour varied across the course of the test.

   Specifying the information shown in reports   (Optional)

ANY-maze includes a number of standard reports such as the Test schedule report and the Animal details report. Depending on the type of experiment you're performing, you may want these reports to show different information. For example, in a water-maze experiment it would be useful if the test schedule report included a test's stage and trial number, whereas in a plusmaze experiment this information would be unnecessary as each animal would probably be tested only once.

You can define which columns are shown on the Test schedule report and which results, if any, are included in the Animal details and Test details reports.

   Defining results reports   (Optional)

Although you can always create results reports using the Results page you may want to define some standard results reports as part of your protocol. For example, in plusmaze experiments you will probably always want to see the number of entries into the open arms and the percentage of time spent in the open arms - perhaps analysed between the treatment groups using an ANOVA.

In this case, you could define a report that shows this information as part of the plusmaze protocol, and the report would then be available, via a single click, in all plusmaze experiments. Of course, you could still use the Results page to perform any additional analysis you need.

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ANY-maze help topic T0035