NeuronAnalyzer2D: How to use MiToBo

I am trying to understand, how to use MITOBO, in particular, the NeuronAnalyzer2D plugin on imageJ.

I checked the MITOBO website but I could not find a tutoria lsetp by step how to use it.
I read also the paper and I would like to reproduce some of the analysis that were used on that paper but It is getting complicated to put my images to work on it.
Can someone guide a bit with the use of that plugin?
Thank you in advance.


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thanks for your interest in the NeuronAnalyzer2D! Unfortunately we don’t have a tutorial or howto yet. My colleague who has implemented the plugin and can best guide you through the first steps is currently out of office. But, he is already informed and will come back to you as soon as he will be back. I think that this will be latest at the beginning of the next week. I hope it is ok for you to wait these few days, but doing so will reward you with the most profound guidance on getting started with the plugin :wink:

Have a nice time


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Thank you very much. I will wait then because I think it could be beneficial for my analysis.

Hello Pablo,

I will try to explain the use of the plugin. So if MiToBo is running and you select the NeuronAnalyzer2D a configuration window is opened for the NeuronAnalyzer2D operator.
First you con configure the detector for neurites. Allow for profile extraction, define molecule names of the different staining channels in the image, select the index of the molecule channels for profile detection along neurites and if present you can try to detect particles along the neurites, which may not work probably on all images.

Think the important step is the Neurite Detector configuration. If you select the button a new window comes up. On top, go to view -> advanced to see all parameters.

Choose the directory with your input files, define nuclei channels. Of course there are a lot of parameters, which are predefined for the images we used. On the MiToBo website you can find some example images, maybe it is a good starting point to try the operator with these images. Did you get the operator running and there are some errors?


Thanks, Danny.
I will try to use it and follow your instruction.