Skip to content

MRI_Neurite_Analyzer

Jump to bottom
Volker edited this page Jun 2, 2022 · 15 revisions

The toolset helps to segment neurites, measure the distances on the neurites to the closest soma, assign each neurite to a soma and to measure the FISH-signal on the neurites.

distance_neurites.png labelled_neurites.png

Getting Started

You must have the ilastik4ij-plugin and the Neurite_Labelling_IJ_Plugin installed. Save the ilastik classifier neurite_segmentation_3.ilp and the toolset neurite_analyzer.ijm into the macros/toolsets-folder of your FIJI installation. Select neurite_analyzer from the >>-button:

toolbar.png

Before using the toolset, please configure the ilastik4ij-plugin. Run Plugins>ilastik>configure ilastik executable location and set the path to your ilastik-executable.

  • the n-button segments the nuclei in the active image
  • the s-button segments the neurites in the active image (this might take a while)
  • the d-button calculate the
Clone this wiki locally