Spine Analyzer

The tools allow to semi-automatically segment dendritic spines in 3D+t images and to measure their volumes and the intensities of the signal within in different channels over time.

You can find the source code in git-hub here.

Getting started

You must have MorphoLibJ installed.

To install the tool download the file spine_analyzer.ijm and put it into the folder macros/toolsets of your FIJI installation. In FIJI, select the spine_analyzer-toolset from the more tools button >>. On the toolset, click on the Install or Update Tool (the rightmost tool of the toolset).

Note: In case you do not have jython installed the first time you run the installation, only jython will be installed. You then have to retsart FIJI and click on the Install or Update Tool again.

After the installation finished, restart FIJI. Select the spine_analyzer-toolset from the >>-button of the ImageJ launcher.

• the first button opens this help page
• the s-button runs segmentation of a spine within a region of interest (ROI)
• the pipette-tool allows to select the label of a spine for the usage with the bucket-tool
• the bucket-tool replaces the label of a spine in a frame with the selected label (select the background to remove a spine in a frame)
• the next button adds a dendrite, on a frame, defined by a polyline-roi
• the first tacking-button tracks the dendrites
• the second tracking-button tracks the spines and gives the same label to a spine in different frames
• the paper-clip button attaches spines to the closest dendrite
• the next button allows to measure the spines in the image
• the last button allows to install or update the spine-analyzer

Usage

The first step is to add dendrites and to track them in the different frames. Once that is done, you can segment spines, track them over time and attach them to the closest dendrite. The last step is to measure the volume and intensity of the spines in different channels over time.

Adding and tracking dendrites

Make a polyline selection on the center of a dendrite, then press the Add Dendrite`- button [F6]``. The first time you do this, the operation will take longer than usual, because the image will be initialized for the tool. Subsequent operations will be faster.

Go to the next frame and repeat the procedure. Then repeat for the next dendrite. Once you added all incarnations of all dendrites you're interested in, press the Track Dendrites-button. The same dendrite on different frames should be displayed in the same color after the tracking.

Hint: If you want to copy a dendrite from one frame to another, choose the rectangle roi tool and click on the roi of the dendrite in the source frame. Change to the target frame. Press ctrl+a followed ctrl+e. You now have a new selection corresponding to the original one on the new frame. You can move it around as a whole using the arrow-keysof your keyboard and you can modify the individual points using the handles. Once done modifying, press the Add Dendrite-button.

Options

• the maximum distance a dendrite can move between two frames in physical units

Segmentation of Spines

Use the freehand selection tool to make a selection around a spine, then press the s-button to segment the spine in 3D on the current frame. Repeat the procedure for the next frame. Do the same for all other spines on the selected dendrites. Then press the Track Spines-button and finally the Attach Spines-button to attach each spine to its closest dendrite.