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Applying transforms so all apparatus maps align

Introduction

If you include multiple apparatus in a protocol then you'll have the option to apply transforms to the apparatus map so they align, what this does and why it is useful, is best described through an example.

Imagine you have the two water-mazes shown in figure 1 and that you intend to use them both in a single experiment (so as to increase throughput).

Figure 1. Comparing or averaging track plots and heat maps of tests in these two apparatus would be difficult because the platforms are in different locations.

As can be seen, the mazes are the same except that in one the platform is in the top left and in the other it's in the bottom right. Now imagine you were to run tests in 20 animals in these mazes, 10 of the animals receive saline and 10 receive a drug and you test 5 of each group in each maze. At the end of you test you want to compare the track plots and heat maps of the two groups. This will be possible, although, of course, some of the plots will have the platform in the top left and some in the bottom right, so it won't be too easy to compare them.

Now imagine you want to plot average heat maps for the two groups, perhaps to compare the time they spent in the platform quadrant during a probe trial. To achieve this ANY-maze will, in effect, take all the heat maps for the animals in one group and stack them up on top of each other and then average the 'heat' through the stack. But because  half the animals in the group had the platform in the top left and half had it in the bottom right, the resulting averaged plot won't really represent the average time in the platform quadrant.

Hopefully, you can now see the problem! The solution is to rotate all of the heat maps in one of the apparatus by 180 degrees, so they then align with the heat maps from the other apparatus, then if they are all stacked up and averaged the result will accurately represent the average time in the platform quadrant, as shown in figure 2, below

Figure 2. By applying a rotation transform to the apparatus with the platform in the bottom right, we can make the platforms align.

Clearly in our example, you only need to apply this transform to one of the apparatus, but if you had another two mazes with their platforms in the top right and bottom left then you'd need to rotate them too. In fact you usually need to choose one apparatus as 'correct' and then adjust the others so they all align.

Of course the apparatus do need to be symmetrical for this work, but usually if you are using multiple apparatus for the same experiment, you'll want them all to be identical - so you wouldn't use a square maze and round one, or one with a large platform and one with a small one (unless of course the purpose of the experiment is to test the effect of the differences in the mazes, but then alignment would be irrelevant).

Details

The actual options available to align the apparatus are:

Usually you will want to rotate the apparatus, but the flip options are useful in situations such as two place preference boxes which are mirror images of each other.

In some cases differences in the distance of the camera from the apparatus will make some apparatus look larger or smaller. There is no transformation available to address this because ANY-maze will automatically compensate for the difference when it creates track plots and heat maps - however, this is most effective if the differences are small, so you should try to make the apparatus images broadly the same sizes, but differences of +/- 10% are OK.

In some experiments you might move a zone such as the water-maze platform, between different tests within the same apparatus. In this case you will need to apply transforms based on the position of the zone, which is described here.

When you show a track plot or heat map of an apparatus which includes transforms, the track plot's menu will include an Apply transforms option. This option is selected by default.

Figure 3. If they're defined, you can easily choose whether or not to apply transforms to track plots and heat maps.

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ANY-maze help topic T0126