Correcting False Merges

Overview

False merges can be corrected by the splitting tool in NeuTu. To start splitting, the user needs to select a body and then enter the split mode, which will set the selected body to the target body for splitting.

After split launched successfully, the control panel will be switched to show the interface for splitting.

Alt+Space may not work on some systems because of its binding to system functions. You can use Alt+Shift+Space instead for such a case.

Detailed Instructions

1. Launch the split mode

  1. Click to choose the body you would like to split in the normal mode

  2. Right click and choose ‘Launch split’ from the pop-up menu.

There is another way to launch. The user might want to use it occasionally:

  1. Press <Launch Split> in the main window.

  2. A dialog box appears. Enter the body ID and press ‘OK’. If there is a body selected, the box will have its body ID automatically to save typing.

2. Find the false merge

If the assignment bookmarks are not provided, open the Body View (3D). Find the false merge by looking through 3D and 2D images. Also, click on the 3D view and hit the ‘z’ key to go to that location in the 2D window.

3. Place seeds

  1. Press R key to turn on seed painting;

  2. Use mouse to paint seeds with different colors on regions that you would like to split. Select the seed color using the 1 through 9 keys. See the color-key guide at the top of the 2D window. Note that you will create at least two bodies during the split operation. The body marked by the red (#1) seeds will keep the original body ID. The non-red body will get a newly generated body ID. The message board displays all body IDs before and after the split.

  3. To delete seeds, select the seed by clicking on it, then press the delete key. You also have an option to select seeds by color or select all seeds from the drop-down menu.

  4. A false merge may occur when boundaries (i.e. membranes) are not visible. You may have to draw seeds around the edges to fill this “leak”. If needed, draw seeds on multiple planes.

4. Execute splits

  1. Execute a split (Press Shift + Space). A progress bar appears as NeuTu performs the split. Inspect the quality of the split and add more seeds as needed and repeat the split.

  2. Open <Split Quick View> to see the split bodies in 3D; rotate and inspect as needed.

  3. Repeat steps 1-3 as needed.

  4. Press <Save Split> when done. A dialog box shows up with options (see below). The default setting is fine for most cases.

  5. New Body IDs are created for new bodies. These IDs are displayed in the message box.

Split View
Options of Uploading Splits

Group small objects: When this option is checked, bodies smaller than the threshold size (in voxels) will be grouped as one body instead of assigning a unique body ID to each small body. Keep main seeds (label = 1): When checked, the main seeds (red) will remain after the split. If not, all seeds will be removed automatically.

Connected component analysis: It propagates the analyses to the body which is outside of the bounding box, or approximately x200*y200*z200 from your seeds when you don’t use the bounding box, and allocates the appropriate body ID for those parts of the body. If you don’t use this option, any parts of the body out of the bounding box keep the original body ID.

Connected Component Analysis

Other Functions

Bounding Box Split

Split is performed in a bounding box drawn by the user. The split is restricted to a limited area to save computing time.

  1. Shift + R key to start the drawing tool

  2. Draw a box by dragging the mouse and place seeds on each body.

  3. When you execute the split (Shift + Space), it only splits in the box.

  4. The box can be expanded by Shift + click on area outside of the current box. Make sure you see the pointing finger icon. If not, shift + R again, and Shift clickto expand the box.

Bound Box Split