MoMA

This page explains the user interface of MoMA. If you want to learn how to install MoMA, you are referred to the [Installation guide](Installation guide). If you want to learn how MoMA data needs to be organised, and how MoMA can be run, you are referred to our [Quick user guide](Quick user guide).

The MoMA user interface

After MoMA launches, you will see a similar window as the one depicted above. Main user interface elements are:

• Three image viewers that (initially) show three consecutive time points.
• A time slider which can be used to navigate through the time series. (Hint: press t to focus on the slider, then use the cursor keys to navigate back and forth in time!)
• A double slider (green) to select an optimization range. This feature comes handy if a very long time series has been loaded. In short: when the button Optimize is clicked, only the time points chosen by this slider will be tracked (find some additional details below in subsection 'leveraged editing').
• Button Optimize starts the segmentation and tracking pipeline. Results will automatically be visualized.
• Button Restart resets MoMA's tracking.
• The export buttons do the expected and will ask additional questions...
• At the very top, there are two additional tabs: the 'Cell Counting' tab gives an overview of how many cells and cell divisions have been detected throughout the dataset, and the 'Detailed Data View' allows you to have a closer look at the image intensities along the wiggly green line at time point t. It also shows which segment hypotheses exist for this time point (rectangles that stack at the top of the plot).

Leveraged Editing

Once the tracking is performed (button Optimize has been pushed), MoMA will show segmented cells within the image viewers (see sample image above), and all cell assignments between time points (mappings are shown in blue, divisions in orange, cell exits in red). Use the time slider to verify if the automatically found solution is correct.

In case you find a tracking error, you can conveniently interact with the found tracking (leveraged editing) in the following ways:

• Hovering over any of the image viewers highlights possible cell segments. Clicking on one of those forces the tracking to include the selected segment. (Shift+click forces any segment below the mouse cursor to be excluded from the found tracking solution.)
• Similarly one can interact with assignments. The assignment views can switch from OPT (showing the found optimal tracking solution), to be showing a large set of alternative mappings, divisions, and exit assignments. These assignments can be filtered for better visibility and then, as explained before for segments, be forced or excluded by a simple mouse click.
• The text field labeled with 'I see ? cells!' can be used to enforce tracking solutions that contain precisely k cells at the time point currently shown in the image viewer labeled t.
• If you want to exclude that model resolves during leveraged editing change certain time points or any assignment between to consecutive time point, the check boxes to the right of the label Correct are: can be used. Select the columns that should become immutable and click on the button labeled set. The button reset would remove this immutability constraint for selected columns.
• Last but not least, the button <-all would set ALL time points [0,t] to become immutable. Additionally, in case the 'opt. range'-slider is selecting a subset of the loaded data, the selected optimization range will jump ahead such that the beginning of the new optimization range aligns with the current time (of the time slider).

Keyboard Shortcuts

Shortcut	Function	Shortcut	Function
t	Focus on time slider	a	Show Cell Counting Panel
r	Reset optimization (tracking)	s	Show Segm. & Assignment Panel
o	(continue to) Optimize	d	Show Detailed Data Panel
v	Switch channel to show at 't'	b	Toggle show segment annotations
?,[0-9]	I see ... cells!	e	Export data...

Keyboard + Mouse

Shortcut	Function	Shortcut	Function
click	Force segment / assignment.	shift+click	Hide all assignments below mouse. (Available in AssignmentView.)
ctrl+click	Avoid segment / assignment.	right-click	Show all hidden assignments. (Available in AssignmentView.)
click+drag	Filter by min/max cost. (Available in AssignmentView.)	double-click	Enter min/max cost via textboxes. (Available in AssignmentView.)
shift+ctrl+click	Prune tracking starting at segment.