Count_Spines_On_Dendrite - MontpellierRessourcesImagerie/imagej_macros_and_scripts GitHub Wiki

The tool allows you to draw the path of a dendrite, manually select the spines and count the number of spines in each group.

count_spines_on_dendrite_large.pngcount_spines_on_dendrite_zoom.png

You can find the source code of the tool here.

Getting started

To install the tools, drag this link to the ImageJ launcher window, save it under macros/toolsets in the ImageJ installation and restart ImageJ.

Select the Count_Spot_On_Dendrite toolset from the >> button of the ImageJ launcher.

count_spines_on_dendrite_toolset.png

  • the first button ? opens this help page

  • the O-button opens the first channel of a .czi image.

  • the D-button convert the current selection into a ROI of the dendrite.

  • the S-button enable a tool that allow to click on the image to select a spine.

  • the C-button count the number of spines of each group and ask for a directory to save the ROIs.

  • the keys 1-5 on the keyboard adds the currently selected spine to the group 1-5 and adds it to the ROI Manager.

Options

You can open the options-dialog by right-clicking on a button.

  • O-button Option : You can change the LUT of the opened image and also invert the LUT
  • D-button Option : You can change the radius of the correction around your selection
  • P-button Option : You can change the radius of the circle of the spines selection

Usage

  1. Click the O-button and select your czi file in the dialog,
  2. Take a line tool and quickly draw a dendrite (Freehand line works well),
  3. Click the D-button, your selection should now be corrected and added to the ROI Manager as "Dendrite"
  4. Click the S-button to enable the tool,
  5. Click on the image on a spine, then press a key between 1 and 5 to add that selection to that group.
  6. Repeat (5) for each spine
  7. Click the C-button and give it a directory if you want to save the ROIs