Getting started:

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Growth_Cone_Visualizer is a program that visualizes "Growth Cones" in the form of a diagram. It is programmed with the ImageJ software and it is presented in the form of an interactive graphical interface.

To install the toolset, download draw_growth_cone_diagram.ijm and put it into the folder macros/toolsets of your FIJI installation.

Select the "draw_growth_ cone_diagram" toolset from the ">>" button of the ImageJ launcher and then you will have the buttons: ?, d and b in the imageJ toolbar.

The Growth Cone Visualizer Software is an imageJ-marco toolset that visualizes the morphological variability of neuronal growth cones.

In a biological context, neuronal growth cones are located at the end of axons. These highly mobile structures will navigate the nervous system under the control of external stimuli such as guide molecules to find their biological targets and form functional synapses.

The shape of the growth cone is highly dynamic to allow for growth, pause, and reversal events that occur in the axonal direction.

Indeed, this tool was developed to visualize variations in the morphology of growth cones following various disturbances such as genetic mutations, exposure to external stimuli or to drugs.

As indicated, GC-Visualizer is represented by three buttons (3 macros) in the imageJ toolbar, namely the: ?, d, b buttons as indicated by the following figure (Principal Graphical Interface of ImageJ):

• Button ?: is the software help (an url to this page)

• Button d: draws a growth cone diagram from the ROIs in the ROI-manager

• Button b: draws a growth cone diagram for each ROI-set (zip-file) in a folder

Right-clicking the "d"-button opens an options-dialog that allows the choice

• of plotting the baseline
• of the output image display color (image in RGB color or in grayscale)
• of the nature of the palette colors
  • The chosen color palette can be sampled linearly, affine or nonlinear (parabolic) in RGB mode. Additionally the options-dialog allows to change the options of the montage of multiple growth-cone diagrams.

Clicking the b-button, executes the batch-processing. The tool will request the path to the data containing the input ROIs. The result is a graphical output including all the ROI-sets in the form of an image. This is generated by putting side by side the growth-cone diagrams of the ROI-sets. Each roi in a ROI-set is graphically represented by an outline whose chroma depends on the chosen color palette (LUT) and on the sampling step of this palette.

**Remark: ** To see the scale of the chosen color palette (spectrum), close all images and do the following command: ImageJ → Image → Look Up Table → then choose the palette's name.

By pressing the b-button on the toolset, we obtain the results as indicated below:

Results

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1. Result in Grayscale (Default) Look Up Table Mode:

2. Mode RGB Look Up Table with linear sampling:

3. Mode RGB Look Up Table with nonlinear sampling:

4. Results in the case where there is only one ROI-set in a compressed file and LUT linear sampling as an input:

5. Results in the case where ROI-sets are in a compressed files,LUT linear sampling with one color (Red) as following:

6. Results in the case where there is only one ROI-set in a compressed file and LUT linear sampling with one color:

7. Results in the case where there ROI-sets come from Tulipe image and which are in a compressed file and LUT linear sampling with one color (Green):

Notes

This software application allows to visualize the different ROI-sets using different color palettes and also using different linear and non-linear sampling modes.

Publications using the tool

1. Bonnet, M., Roche, F., Fagotto-Kaufmann, C., Gazdagh, G., Truong, I., Comunale, F., Barbosa, S., Bonhomme, M., Nafati, N., Hunt, D., et al. (2023). Pathogenic TRIO variants associated with neurodevelopmental disorders perturb the molecular regulation of TRIO and axon pathfinding in vivo. Mol Psychiatry. 10.1038/s41380-023-01963-x.