The 3D environment: Getting started To open the 3D window, click the button in the Trace or the Workspace ribbon.

Transcription

1 Getting started To open the 3D window, click the button in the Trace or the Workspace ribbon. Neurolucida 360 1

2 Navigation Define a new pivot point to rotate around the point of your choice. Drag to rotate. Scroll the mouse wheel to zoom. Hold down Shift and drag to pan. To use the pivot point, click the icon in the toolbar then click in the image to place the new pivot point. You can now rotate (by dragging the mouse) from your chosen point. Neurolucida 360 2

3 SCENE DISPLAY mode If there is no file open, click the Open Tracing or the Open Image icon. MODES Open images, stacks, or data files. SCENE mode Get help specific to this mode. Options vary for each mode. Neurolucida 360 3

4 IMAGE DISPLAY mode To navigate the 3D environment, use the mouse: Drag to rotate. Scroll the mouse wheel to zoom. Hold down Shift and drag to pan. Once your file is loaded, the IMAGE panel is displayed. For typical stacks, you have the option to view the stack as cross-sections (IMAGE SLICE) instead of 3D VOLUME. For images with very large Z spacing and small XY spacing, select SECTIONS. Show surface as Min projection The image foreground is brighter than the structures (e.g., brightfield). Max projection The image background is darker than the structures (e.g., fluorescent & confocal). Partial projection Display a subset of the data in X,Y or Z. Alpha composite Adds 3D depth and more detail. Channel Apply the adjustments to a single channel in a multichannel image. Adjustments are not saved. Gamma/black point/white point Enhance 3D display only. Adjustments are not saved. Options will vary for IMAGE SLICE and SECTIONS Image sync with 2D Apply changes made via Image Adjustments in the 2D window (typically for multichannel images). Neurolucida 360 4

5 SOMAS mode DETECT SOMAS EDIT SOMAS Click to access the SOMA mode. Click to display the editing options. Define the size of the detection region for interactive detection. Soma count Increase the value to minimize soma flow into dendrite. You can also select individual somas by clicking them. To detect individual somas interactively, click in the image. To adjust Interactive search region (represented by the cursor size), hold down Ctrl and scroll the mouse wheel. Options visible when somas are selected. Change soma color. Neurolucida 360 5

6 TRACE TREES mode There are three tracing methods and you can easily switch between methods while tracing. Don t forget to check Partial Projection in the IMAGE panel before you start tracing SMART MANUAL Use the mouse to trace USER-GUIDED Choose from 3 detection algorithms. Click a button to trace AUTOMATIC Trace based on the settings below (click SHOW SETTINGS). Automatically re-centers last click. Choose from 3 detection algorithms. Review seed detection settings to improve tracing. Neurolucida 360 6

7 EDIT TREES mode Use the Edit Trees panel to connect or detach branches, define an origin point, or specify tree types for later analysis. Click to display the editing options. You can also select individual trees by clicking in the image. Clean up tree fragments and unconnected branches. To define the origin: 1. Click the POINTS button. 2. Click a point in the tracing. 3. Click the button to set the origin. Select a type for later analysis. Change tree color. Visible when trees are selected. Neurolucida 360 7

8 VARICOSITIES modes DETECT VARICOSITIES EDIT VARICOSITIES Click to display the editing options. Click to access the VARICOSITIES mode. You can also select individual varicosities by clicking them. Detection based on these settings Change color. Restricts the automatic detection to a single branch instead of the entire image. Options visible when varicosities are selected. Neurolucida 360 8

9 DETECT SPINES mode Only available when at least one tree is traced. Spine count. Refine default settings after initial detection. You can also detect individual spines by clicking in the image. Click to define your own settings. Click to classify automatically (4 types). Uncheck to use spine total extent instead. Neurolucida 360 9

10 EDIT SPINES mode Click to display the editing options. You can also select individual spines by clicking in the image. Confirm spine head or reassign to a different branch. Classify manually. Visible when spines are selected. Neurolucida

11 SYNAPSES modes DETECT SYNAPSES Only available when at least one tree is traced. Synapse count. EDIT SYNAPSES Click to display the editing options. Refine default settings after initial detection. Click to detect automatically. Select the correct channels. You can also select individual synapses by clicking in the image. Visible after detection. Use these filters to refine the detection. Visible when synapses are selected. Neurolucida

12 SETS mode Use the Create sets panel to group structures forming a single neuron for instance. The sets can be used for analysis in Neurolucida Explorer. Click to access the SETS mode. 1. Select the objects to group. You can also select objects individually by holding down CTRL and clicking them in the image (or drawing a marquee). 2. Create sets manually or automatically. manual Distance soma-tree ending automatic 3. Optional: Edit the sets. Neurolucida

13 EDIT MARKERS mode You can edit markers in the 3D window, but markers must be placed in the 2D window. Markers count You can also draw a marquee to select one marker or multiple markers. Visible when markers are selected. Neurolucida

14 EDIT CONTOURS mode You can edit contours in the 3D window, but contours must be drawn in the 2D window. Select contours by type. Visible when contours are selected. Neurolucida

15 Analyze data in Neurolucida Explorer Once you're satisfied with your tracing, you can view and analyze your data quickly. Click. Neurolucida

16 CREATE MOVIES Easily create video clips (mp4 format). Slide to define an angle for rotation. Set the auto-rotation speed. Neurolucida