Finding stalls

Need more help? Here’s everything you need to know about finding stalls:

A Virtual Microscope (VM) allows you to look at real movies of brain blood vessels, acquired using two-photon microscopes at Cornell University.

In each movie, you will analyze a single blood vessel, enclosed within a green outline.

Vessels generally appear white, since the blood plasma is stained with a white fluorescent dye. Blood cells are not stained and therefore appear as black “stripes” inside the vessel.

Under normal circumstances, stripes, i.e. blood cells, are moving freely along the length of the vessel. However, sometimes these cells get “stuck” and prevent blood from flowing. Such a vessel is considered a stall.

To illustrate how a flowing vessel differs from a stall we are using magical zebras (yes, you read that right):

This is a magical Zebra. You can tell it’s magical because it sparkles. It is also a health zebra, which you can tell because the stripes are moving. Only healthy zebras have moving stripes.

When a “magical” zebra gets “sick”, it is still sparkly, but it’s stripes get stuck and no longer move.

We use these magical zebras as a metaphor for blood vessels that are either flowing or stalled. Vessels in the Stall Catchers vessel movies, like the magical zebras, are always sparkling (white dots flicker as the microscope changes focus), but the black stripes can appear either moving or stuck. When at least one “stripe” appears stuck, we call this vessel a stall.

Step-by-step guide to annotating vessels:

  1. To start annotating go straight to the “Virtual Microscope” and start watching a vessel movie.

    Movies are autoscrolled (auto-played) by default. If you’d like to scroll the movies yourself, at your own speed, uncheck the “Autoscroll” checkbox above the vessel movie. To scroll the movies manually, use the slide bar underneath the vessel movie.
  2. Next, find the vessel to be analysed. Play the movie, paying attention only to the area within the green outline. Usually (but not always) around the middle of the movie, a white vessel will appear in the center of the enclosed area. This is your vessel. Note that depending on its 3D shape, only a part of the vessel may be seen in any one layer. However, by scrolling forwards and backwards you should see how the shape of the vessel follows the centre of the green outline.
  3. As you scroll through the movie, you may see black “stripes” inside the vessel, which are either moving (change position between layers) or stuck (do not change position in multiple layers). If there is at least one black “stripe” that is stuck and does not change position in multiple layers, the vessel is stalled. When this happens, double click on the black “stripe” directly in the movie to annotate the vessel as stalled. If the “stripes” are moving and no stuck stripes are present, the vessel is flowing. In this case, click on the “Flowing” button to annotate the vessel as flowing.
  4. Important: Make sure you look through the entire movie before making a decision!
  5. Note that in some movies individual the black “stripes” are less evident, even if the vessel is flowing. That is normal and depends on the focus of the movie. What you should concentrate on is “stripes” or “gaps” that are present within the vessel and don’t move. If there is at least one such “gap”, the vessel is stalled.
  6. After you have given your answer, you’ll be shown feedback. We call this feedback “Vessel Talk”. Here you will find out whether your answer was right or wrong, in the cases of “calibration movies” (ones that have already been seen and annotated by researchers). When we don’t know the answer, because the movie represents new experimental data, then we will show any community answers and comments. If any stalls were present in the movie, these will be indicated with red dots directly over the stalls in the vessel movie. To see the stalls indicated by the red dots, you may need to move the slider to the red zone on the slider bar, which indicates the layers where the stalls were observed.
  7. Feel free to add your own comments in Vessel Talk (both for “expert” and regular movies) to help fellow stall catchers!
  8. When you are ready to move on to the next movie, click “Next” and keep going!

Tips:

  • Make sure you look through the entire movie before making a decision. You can replay the movie as many times as you like! (Or just leave the “Autoscroll” box ticked, and it will keep looping through the movie.)
  • If you prefer not to see feedback and Vessel Talk after each movie, untick the “Show feedback” box above the vessel movie.
  • There might be multiple vessels crossing the green area during the movie. That’s normal - after all, there is a tight network of blood vessels in the brain. However, you should pay attention only to a single vessel, which follows the centre and is fully contained within the green outlined area.
  • In some movies, individual blood cells (black “stripes”) will be more obvious than others. That’s normal. Concentrate on finding any “stripes” or “gaps” that are not moving, indicating a stall.
  • Stalls are rare. We have included a fair sample of stalled vessel in our “calibration movies”, but as new vessel data (“real movies”) comes along, only a small percentage of them will be stalls. Do not be disappointed if you don’t discover stalls in real movies for a while, and keep a keen eye out for them! These are significant finds and the very few you discover could be carrying important clues to Alzheimer’s disease!
  • Sometimes vessels may occur at awkward positions, such as “bumping” into the edge of the image. Nevertheless, do your best to follow the entire visible area of the vessel layer-by-layer and look for signs of stalls.
  • Some vessel segments are so small, they might be difficult to interpret. However, always try to find a vessel fully contained within the enclosed area, however small, and look for “stuck” stripes.
  • Some movies may appear very “noisy” or “grainy”, which makes it more difficult to identify a stall. Such movies might require a more careful examination, particularly to discriminate between actual movement in the vessels and motion artifacts (“fake” motion) created by the flickering of the noise in the image. Nevertheless, concentrate on the vessel to be analysed, and look for stripes that are not changing position across layers. The more difficult movies are worth more points ;)
  • Do not worry about getting each answer right! Each movie will be seen by multiple participants, ensuring we arrive at the right answers together.

Have fun!!!