MRI_Neurite_Analyzer

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.

Getting Started

You must have the ilastik4ij-plugin and the Neurite_Labelling_IJ_Plugin installed. Save the toolset neurite_analyzer.ijm into the macros/toolsets-folder of your FIJI installation. Download and unzip the ilastik classifier and the training images. Unzip the archive in the macros/toolbars-folder. Select neurite_analyzer from the >>-button:

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 first button opens this help page
• n-button: segment the nuclei in the active image
• s-button: segment the neurites in the active image (this might take a while)
• d-button: calculate for each point on a neurite, the length of the shortest path along the neurites to the closest soma
• l-button: label each point with the label of the closest soma following a path on the neurites
• f-button: detect the FISH spots and measures the distance along a neurite to the closest soma and the label of the neurite
• bn-button: batch segment the nuclei, segement the nuclei in all the images in all direct subfolders of the input folder
• h5-button: batch export the neurite images as h5-images, optionally apply histogram equalization
• i-button: the button does nothing, but remind the user to use ilastik for the neurite segmentation
• bs-button: batch convert the output of the ilastik segmentation into ImageJ rois
• bd-button: batch calculate the distances and the neurite labelling
• bf-button: batch detect the FISH spots and measure the label and the distance to the soma
• b-button: run all the batch steps after having segmented the neurites with ilastik, i.e. bn, bs, bd and bf.