ON THE MOVE — data in the spotlight

One of the greater challenges of showing imaging data is the movement of particles, cells etc. These days you can submit videos alongside your manuscript, however some journals will ask you to refrain from it (e.g. Journal of Neuroscience) and your audience may not always be able to access it (or may consider it too much hustle). So until videos become the integral part of the pdf file, let's look at the options of depicting it in still images.

1) kymograph

A golden standard in the neuroscience field. Briefly, kymograph is a graphical representation of distance as a function of time. To researchers not familiar with it I like to show this graphic visualizing train transport, from 1885, which helps grasping a concept behind the kymograph.

Reason why this is a very powerful visualizing techniques is because you can read many transport parameters from it, like: direction of movement, speed of the particle, number and length of pauses, as illustrated in Marinković et al. 2012:

The main problem with the kymograph is that it works best when transport happens along one axis. If your particles are moving at multiple angles kymograph may not be the best solution.

2) single frames

This is the very classical approach to showing changes over time. Typically you split the movie into single frames and present them in vertical or horizontal order.

In those examples moving particles have been pseudocolored to focus attention on them. Alternatively you can use arrows to drive readers attention. This particular approach is commonly used when working with tracing, for example in cell migration.

3) overlay

This method is a variation of single frame representation and is very powerful when dealing with densely labeled samples. Basically, you overlay consecutive frames of the movie (at a selected interval) and pseudo-color them, in the following fashion:

frame 1 - blue

frame 2 - green

frame 3 - red

When you overlay those 3 frames, you will get the following image (Plucinska et al. 2012)

Stationary particles appear as white and the arrows point out to moving particles which appear in color (respectively to the coloring scheme above). If the time frames you choose are small and the environment is not too crowded you can see movement of individual particles. In this particular approach it is important to use primary colors (red, green, blue) - in the overlay they will appear as white, which is not the case if you use off colors.

4) cartoons

In paper by Marinković et al. authors had to deal with another problem. While they look at the axon in which transport happens bidirectianly, the density of the labeling would blur the overall images over-representing stationary mitochondria.

Therefore they chose to draw a line in the middle of the image (grey dotted line) and show how many mitochondria crossed it over time (additionally indicating the direction by green or magenta color).

To summarize, when you want to show your time lapse data, you have to consider following factors:

- movement directionality (bi-, multidirectional)

- labeling density

- speed of movement (generally slow moving particles will appear better as single frames, as you can put a "timer" on the images)