- Technical requirements
- Hints for common problems
- Keyboard Shortcuts
- How to Play: Navigational Tools
- Change Resolution
- Zoom In/Out
- Translate Camera
- Rotate Camera
- Invert Colors
- Adjust Contrast
- How to Play: Tracing Tools
- Virtual Finger
- Changing Viewable Volume
- Connect-the-dots mode
- Labeling Axons and Dendrites
- Delete Node/Branch
- How to Play: Common Errors/Mistakes
- False Positives
- Scientist Comments
- We currently support all recent versions of Chrome, and Firefox versions 47 and higher. The most current Safari on Mac should also function. We plan better support for Edge as soon as possible, but we're not there yet. Unfortunately, Internet Explorer 11 and earlier are not supported.
- It's highly recommended, but not required, to play with a mouse and laptop/desktop. We don't think the game will work well on a touchpad, but we'd like to hear about your experiences if you try it.
- We don't currently support mobile devices or touchscreens, but we hope to in the future.
Hints for common problems
- Created account, but unable to log in
Check the email you registered your account with. You should have received an activation link. Click the activation link to activate your account and log in.
- The game loses my place when I go to another part of the site or close and reopen the page.
Make sure you have cookies enabled. Progress is only saved across machines if you create an account.
- What if nothing shows up on screen?
Try these solutions first:
- Try clearing your browser cache. Sometimes when we update the websites, certain files get out of date and cause errors unless a fresh copy is fetched. Instructions to clear the cache for a specific site on Chrome and Firefox. can be found here. For Safari on Mac, Go to Safari->Preferences->Privacy->Manage Website Data. Search for mozak and ‘Remove’ the data for the site.
- Certain browser extensions (like popup blockers) or anti-virus software may cause errors when trying to run the application. If you have such programs installed and are encountering problems with the site, consider adding a security exception to those programs.
- I went through those steps and am still having problems.
- V : Switch to Virtual Finger tracing mode
- C : Switch to Connect-the-Dots tracing mode
- D : Switch to Delete Single Node mode
- B : Switch to Delete Branch mode
- U : Undo trace or delete action
- R : Redo trace or delete action
- A : Toggle auto z-adjustment for Connect-the-Dots tracing
- K : Toggle view mode to see disconnected traces
- P : Toggle view modifier to see axon and dendrites as different colors
- Ctrl and [, then F5 (or reload page): Restarts tutorial from the beginning
- Ctrl and ], then F5 (or reload page): Automatically completes tutorial
- Arrows ←↑↓→ (all computers) OR 4, 8, 2 and 6 on Num Pad with Num Lock off (PC only): Translate current view
- Shift and Right Mouse Button click/hold and drag: Another way to translate view(moves view in direction of mouse drag)
- Spacebar : Re-centers the view along X, Y and Z axis, and focuses on the front of the challenge
- F : Fullscreen toggle
- Google Chrome, Mozilla Firefox and Internet Explorer (when in Fullscreen mode): Ctrl and + / Ctrl and -: Increases / decreases the font size
Thank you so much for trying our beta. This stage of beta is an open beta, so be sure and tell your friends about Mozak. Our current goal is to be able to give Mozak players (non-experts) the tools needed to construct expert-level neuron reconstructions.
Here are some things you can do to help us reach this important goal:
- We need you to trace as much of the neuron as possible.
- You can submit your bugs here. For maximum helpfulness, please include browser version, operating system, and any error messages you receive; if you want help gathering that information, check here.
- You can submit suggestions here to help us make Mozak more awesome and fun; after all, we're trying to make a game people will enjoy while helping advance science. Strive to be honest but constructive. We've got plenty of things on our list already (we're all gamers in our spare time), but even if you make a suggestion you've already thought of, your input helps us prioritize future work.
- We're a small team, but our enthusiasm is mighty. Your patience is appreciated.
How to Play: Navigational Tools
Each neuron in Mozak is a single, extremely large, image — so large that your computer would never be able to load the whole thing at once. Mozak cuts it down to size by allowing you to see small parts of the image in full detail, but also letting you view less-detailed versions of the image from farther away, so you can get a better idea what's going on on a larger scale.
The Map View provides an easy way to examine different parts of the neuron quickly, albiet only in two dimensions. Click and drag with the Right Mouse Button to slide different parts of the neuron into view. Use the mouse wheel to zoom closer and further away from the neuron. When you have found a portion of the neuron image needing annotation, click the Edit button (a pencil icon) to load a portion of the neuron into the three-dimensional annotation view.
The Annotation or Edit View is where you'll be able to use the various tracing tools, described below. If you want to move to a different portion of the neuron, click the Map button (a map icon) to switch back to the two-dimensional map view.
If you want to zoom in or out, use your mouse's scroll wheel.
Translate Camera while Editing
In order to look at a different section of the image, use the green arrows on the edges. Your view will move in the direction the arrow is pointing. You can also move this section of the image on the screen with the arrow keys.
Rotate Camera while Editing
To view the neuron from a different perspective, hold and drag with your right mouse button. This is helpful when you feel like you've completed a section and want to view it from another angle, or when you want to get a better look at details that are hidden behind other parts of the neuron.
Rotate Camera while Editing (Mac Trackpad)
If you are using a trackpad that does not have any left and right click buttons, then you can perform the rotate by using a two finger press.
Click the invert tool toward the top of the tools menu. This will invert the colors, which may help you identify difficult-to-see sections. If you've inverted the colors, your bounding box will change color from yellow to purple so you can see it better on a light background.
Another tool that will help you see difficult-to-see sections is the contrast slider at the top of the screen. Drag it to the right to make the image lighter, to the left to make it darker.
How to Play: Tracing Tools
The neuron reconstructions you build in Mozak are made of a skeleton of nodes connected by lines. You can also see the reconstructions that other players have made. These contributions are part of something called consensus, which is the common work that multiple people have contributed to.
By default, you're in Virtual Finger mode. Simply hold your left mouse button while dragging your cursor along a branch of the neuron, then release and the computer will automatically follow it. This is the tool you'll use for most of your tracing.
If you move your mouse near a part of the neuron you've already reconstructed, you can highlight a node to extend from, which will make its node appear larger. When you extend from a node with Virtual Finger, the start of the branch you trace will be connected to that node.
After you start tracing, if you move your mouse near a part of your reconstruction, you can highlight a node to connect to, which will draw a blue highlight around it. When you connect to a node with Virtual Finger, the end of the branch you trace will be connected to that node.
Changing Viewable Volume
There are times where virtual finger will result in very poor looking traces, you may find the nodes and lines generated jump around in bizarre ways. This is most likely due to the tool capturing noise in the region and different z-depth. To resolve this, try reducing the viewable volume virtual finger searches over.
While in virtual mode use these controls to adjust the volume:
- Shift + Mouse Wheel: Increase/Decrease the depth of the viewable volume.
- Alt + Mouse Wheel: Change the z location of the volume.
Some parts of the neuron are too dim to trace with Virtual Finger. When you select the connect-the-dots tool, you shift from a 3D view of the neuron to seeing a single 2D z-slice through the neuron, somewhere between its front and its back. In this view, an individual neuron branch looks like a series of bright spots and lines on neighboring z-slices.
You can move between slices by rolling your mouse wheel up and down. When you see one of these bright spots, you can place a node on it by left-clicking, and build up a branch by following the branch between planes and dropping nodes in a line as you go. Right-click when you're done with a given branch to put those nodes into your reconstruction, and once you're completely done with connect-the-dots, click the button again to switch back to Virtual Finger.
You can use the connect-the-dots tool to connect two branches. But be careful to not make a loop! Sometimes its hard to tell if connecting to an existing node will make a loop. Mozak will warn you with a message if it would. You'll also see any potential loops highlighted in bright red.
In some situations with very close branches you'll need to place a node in a location that triggers the loop detection. If you're very certain that the node is in the right place, you can over-ride loop detection by turning Snap to Node off in the Settings Menu. Mozak will still warn you about potential loops, but you'll be able to place nodes. Remember! Neruons don't have loops, so neither should your reconstruction.
- Mouse Wheel: Change z-slice
- Hold down '<' + Mouse Wheel: Zoom in and out
- Left Click: Place a node
- Right Click: Finish placing nodes and end branch
Labeling Axon and Dendrite
When using Connect-the-dots or Virtual Finger, the traces you make are not labeled as either dendrite or axon. Using the labeling tool, you can select traces and choose whether they are dendrite or axon. Look at the page here to learn more about axon and dendrites. Being able to identify the correct type to use is one of the big challenges to the creation of high quality neuron reconstructions.
The Labeling tool allows you to select any trace. Once selected, a dialog appears with a choice of label and two buttons, "Branch" and "Neurite Arbor". These two buttons choose how much of the trace you would like to label. The "Branch" selects nodes in the current branch of the trace. If you would like to select more nodes, the "Neurite Arbor" button selects all the current branch and all the branches connected to it leading away from the soma. Use the Undo tool to reverse labeling changes.
Deleting Nodes, Edges, and Branches
Sometimes you'll make mistakes, but you can fix them. For small mistakes, select the eraser tool, then left-click to delete a single node. You can also use this to delete individual edges, just mouse over and click just like a node.
For bigger mistakes, you can delete a whole branch at a time. Select the trash tool, then left-click on the branch to delete.
How to Play: Common Errors/Mistakes
Z-jumps happen when Virtual Finger gets confused about what z-slice a branch is on. It creates a segment that inappropriately stretches between z-slices that are great distances away. You can use the delete tool and delete single nodes to fix this issue.
Tracing False Positive
Sometimes you will encounter strands that look like a part of the neuron but are not really. These are false positives and should be avoided as the scientists need to cleanup/remove them during their evaluation. As a rule of thumb, if the strand you are looking at does not eventually connect back to the main neuron structure you should avoid tracing it.
Comment area looks empty
If the bounding box marked by a comment looks like it's empty, try using Connect-the-Dots mode to look through each z-slice for things you can't see in 3D. If you still can't see anything, try inverting colors or dragging the contrast slider to get a better look. Use the H key to turn off consensus traces if those are interfering.
What is consensus?
Consensus is an on-going process that looks at all the traces that users have contributed to a particular neuron and merges together branches where multiple people have traced the same branch. This results in a single output reconstruction that eventually gets sent to the scientists at AIBS for analysis. Any particular neuron might have several consensus runs applied to it during the time it is open.
Why don't I have a score yet?
Scores are calculated after a consensus run has finished. Depending on the number of people that have traced on a neuron, it can take several hours or even a few days for it to complete.
What do the colors mean?
The colors of the traces you see will differ depending on what view mode you have turned on. You can access and change the view mode in the settings menu in the top right corner.
If you have the 'Trace View' turned on:
Your most recent trace
If you have the 'Connect View' turned on:
A neurite that is already connected back to the soma.
A neurite that still needs to be connected back to the soma.
What does the option 'Z-Clip in CtD' do?
This option clips the traces that are not close to the current z-slice you are viewing when you are in Connect-the-Dots mode. It does the same if in Virtual Finger mode and you have adjusted the viewable volume using the Mouse Wheel while either the Shift or Alt key is held down. It can prove to be a very handy tool option to remove extra visual noise when identifying faint branches. One important note is that the 'Thick Lines' option must also be turned on for it to work. The downside is that 'Thick Lines' might reduce application performance.