Detect Spines Panel (3D)

Only available when trees have been traced.
See Detecting and classifying spines (3D) or the Spines tutorial (PDF) for step-by-step instructions.

If you want to associate spines with a specific color channel, select a single channel using either the Channel panel on the left side of the 3D environment window or the Image Adjustment tool (on the Image and Workspace ribbons) in the main window (2D).

Detection

Outer Range field

Maximum distance between the dendritic surface and the potential top of the spine head.

• Spines that extend beyond that range are cut off at that distance.
• Set to below 2.5 microns for regular dendritic spines.

Minimum Height field

Minimum distance between the dendritic surface and the furthest voxel identified for the spine.

• Useful to direct the software ignore protrusions that are too 'flat' to be considered spines or to compensate for minor tracing inaccuracies.

Detector Sensitivity field

Adjustments are useful for manual detection of spines that are too light or dark based on the original image intensity.

• 100%: Original image intensity is used.
• Above 100%: Pixels appear brighter to the detector.
• Below 100%: Pixels appear darker to the detector.

Minimum Count field

Works in conjunction with Minimum Height to ignore objects that are too small to be considered spines.

• 10 voxels is the default because an object with a volume smaller than 10 voxels is considered too uncertain to be taken into account for most resolutions.
• Also applies to objects that are not attached to the dendritic surface. Useful for discarding small structures that may arise from background noise.

Keep existing spines checkbox

Check this box if:

• You detected spines manually prior to using Detect All.
• You detected some spines, then changed spine detection settings and plan to detect more spines using Detect All. Checking the box keeps the previously detected spines.
• You notice that, when you click a spine to manually detect it, the model of an adjacent spine is removed. This may happen with spines that touch each other. Keep existing spines prevents detection of the new spine from removing the existing one.

Filter image noise checkbox

Check the box if the image/image stack shows shot noise or background staining/fluorescence; it will help minimize its effects on the data acquired.

Detect All button

Automatically detects spines based on the settings defined in the Detection portion of the window.

Reset button

Resets spine-detection settings to their default values.

Clear Last button

Deletes the spines detected by the previous round of spine detection.

Click image to detect all on nearest branch checkbox

Restricts automatic spine detection to a single branch instead of all defined trees in the image.

1. [Optional] Adjust the detection settings in the Detection portion of the window.
2. Check the box next to Click image to detect all on nearest branch.
3. Click near the desired branch. Spines on the that branch are automatically detected.

Classification

Keep existing classifications checkbox

This option allows you to classify additional spines without changing the spine types for structures that have already been classified.

This is particularly useful in the refining phase of spine classification: you can add spines and set their type manually without losing the classification of the spines already detected and classified.

Classify All button

Spines are classified into canonical types (mushroom, stubby, thin, or filopodium).

Color-coding is applied to represent the spine type.

• To change the default classification settings, click the Settings button to open the Spine Classification Settings Panel (3D).
• To re-classify individual spines manually, click Edit and use the Edit Spines panel.

Settings… button

Spines are classified into types using a combination of measured values and derived ratios that you can modify in the classification settings panel that opens by clicking this button.

See Spine Classification Settings Panel (3D) for details.

Automatic classification color-pickers

Change the default colors assigned to each spine type by pulling down the color-picker and choosing a different color. The change applies to all spines of the same type.

To re-classify individual spines manually, click the Edit button to open the Editing spines (3D) panel (see Editing spines/Classifying spines manually above).

Options

Center after each manual detection checkbox

Use to avoid panning manually while tracing. The last point clicked is automatically re-positioned at the window center.

Show axial smear correction checkbox

Neurolucida 360 software displays the corrected thickness of the tree. Axial smear is automatically calculated after each detection.

Showing axial smear correction only modifies the display of the model; it doesn't affect the data.