Create ROIs from Scratch

NeuTu provides a preliminary interactive tool for creating a new ROI from scratch. The user can use the tool to draw a draft ROI with mouse clicks and convert the draft into the DVID ROI format through NeuTu.

Projects and ROIs

The best way to think about ROIs is existing in two forms, a "source" form composed of points in an ROI project, and a "compiled" form composed of a finalised 3d structure. The ROI tool is designed to build ROI sources from points, and when the "Create DVID ROI" button is pushed, it compiles a finalised ROI form in its own data instance. Compiled ROIs do not depend on their sources (and if one were to keep making more, differently named ROIs with increasing sets of points, one could not trace them back to individual sources).

Getting Started with creating ROIs

If you're already in NeuTu, with a project loaded, bring up the ROI tool using Tools->ROI Tool. This will bring up a control window. The control window can be used to browse the main window and draw 2d shapes in it; the set of those 2d shapes, over a series of slices, are used to build the 3d ROI (shape). Set the "Step" text field to a number of Z-frames you want to typically use between each draw of the objects; the arrows to the right of that move the main window up or down that number of Z-frames. Meshes do not need to be pixel perfect (they should not be; that will generate an overcomplex mesh that will be inefficient to work with).

Toolbar Shortcut

Before you make meshes, you'll need to make an ROI project (these are shared between users) using the ROI tool window.

ROI Tool Window

The "L" key enters ROI painting mode. If you drop your first node, then click with your off-mouse-button to leave the mode, and then select the node to extend it by mouse clicks.

If the linkage between two nodes is broken (e.g. when deleting a node in-between), SHIFT-select the two nodes you want to link, and hit C.

Your process for drawing ROIs will be to draw boundaries on one Z-frame, use the control window to move a certain number of Z-frames up/down, and draw boundaries on that Z-frame, until you hit the end of the object in both directions.

When you're done, you can hit "Create DVID ROI" to create the actual DVID ROI. You can also hit the "Upload" button to save the current ROI drawing and continue to work on it later.

Viewing the ROI

Once you've created this as an ROI, you can preview it in the 3D Body View window (click on the (H)Mesh or(L)Mesh button from the main window), by going to the ROI tab (yours should be in the list).

When there are many ROIs available, it may take a while for the ROI list to show up.

You can also view the ROI in the 2D window by adding the name to the settings dialog.