User Interface
Menu Controls
This section refers to the menu bar that exists at the top of both the Cells and Lineage tree window. Selecting an option from either figure will do the same thing
File
| Control |
Description |
| Open |
Opens a prompt to allow the user to select a different dataset or mat file |
| Close |
Closes the figures, if the data is unsaved, asks user to save |
| Load Stain Info |
|
| Save |
Saves updates to the mat file |
| Save As |
Saves updates to a new mat file |
| Print |
|
| Export AVI |
Opens writer and creates an AVI video file |
| Export Cell metrics |
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| Export AITPD |
|
| Export Lineage Window |
|
Edit
| Control |
Description |
| Undo |
Undoes previous action |
| Redo |
Undoes the previous Undo |
| Tree-Interface |
|
| Resegment from Tree |
Opens tool for User edits on Trees |
| Identify Tree Mitosis |
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| Print |
|
| Stop Tree Here |
Clears associations to hulls past the current time on the current family |
| Lock Tree |
Prevents automatic mitosis edits to be made to tracks in the current family |
| Freeze Tree |
Prevents automatic segmentation edits to be made to hulls in the current family |
View
| Control |
Description |
| Show Tree Labels |
Toggles the labels in the Cell window of Hulls in the current tree |
| Color Tree |
Toggles Marker colors in the Lineage Window of tracks in the current tree |
| Draw Only Structure |
Toggles the Markers in the Lineage window of tracks in the current tree |
| Show Off-Tree Labels |
Toggles the labels in the Cell Window of Hulls not in the Current Tree |
| Show Sister relationships |
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| Show Image |
Toggles the render of the Image in the Cell Window |
| Show Next Channel |
Switches through the different fluorescent channels, if exists |
| Show Reseg Status |
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| Show Missing Cells Counter |
Toggles a label in Bottom-Left of Cell Window displaying number of Hulls that should be in current window |
| Play |
Moves the images forward in time |
| Go to Frame |
Allows the user to select a frame to make current time |
| Display Largest Tree |
Makes the Tree with most tracks the current and displays it on Lineage window |
| Display Tree |
Allows the user to enter a Family id to make current |
Mouse/Keyboard Controls
| Control |
Description |
| Dragging a Hull |
Allows user to switch the label(Track association) of two hulls |
| Scrolling Wheel |
Changes the Current Time |
| Clicking on Wheel |
Splits a hull into two Hulls using Gaussian Mixture Model |
| Press F12 |
Toggles the pixels of the Segmentation results |
Cell Window
The Cell Window displays the original phase image with the segmentation result and the Hull ID numbers.
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Right Click Menu Controls
Additional options that appear when the user right-clicks on a hull in the Cells User Interface
| Control |
Description |
| Add Mitosis |
Takes the current Hull/Track and adds it to the Family of another as a sibling |
| Change Label |
Allows the user to change the track association of a Hull |
| Change Parents |
|
| Change number of Parents |
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| Remove Cell(This Frame) |
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| Remove from Tree |
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| Properties |
|
| Phenotype |
Allows the user to select a "Phenotype" to assign to the Hull |
Lineage Window
The Lineage window displays the current family tree which shows all of the tracks that have been associated to the tree by the user or the segmentation algorithm
Right Click Menu Controls
Additional options that appear when the user right-clicks on a hull in the Tree User Interface
| Control |
Description |
| Remove Mitosis |
Takes the current Hull/Track and adds it to the Family of another as a sibling |
| Add Mitosis |
Takes the current Hull/Track and adds it to the Family of another as a sibling |
| Change Parents |
|
| Properties |
Opens a window to show the user values such as HullID, FamilyID, Fist and Last Frame, etc |
